Variant report

Variant	rs17875401
Chromosome Location	chr6:29796265-29796266
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYB	chr6:29796263-29796492	K562	blood:	n/a	n/a
2	E2F6	chr6:29796122-29796732	H1-hESC	embryonic stem cell:	n/a	chr6:29796238-29796245
3	E2F6	chr6:29796171-29796704	H1-hESC	embryonic stem cell:	n/a	chr6:29796238-29796245
4	MAX	chr6:29796210-29796711	H1-hESC	embryonic stem cell:	n/a	chr6:29796288-29796298
5	MAX	chr6:29796244-29796715	H1-hESC	embryonic stem cell:	n/a	chr6:29796288-29796298
6	BACH1	chr6:29795710-29796325	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
HCG4P8	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11758834	0.87[EUR][1000 genomes]
rs11759549	0.87[EUR][1000 genomes]
rs12661487	0.83[AFR][1000 genomes]
rs12662310	0.81[AFR][1000 genomes]
rs12663821	0.81[AFR][1000 genomes]
rs12665345	0.83[AFR][1000 genomes]
rs17178798	0.83[AFR][1000 genomes]
rs17178917	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs17179108	0.95[AFR][1000 genomes]
rs17185132	0.83[AFR][1000 genomes]
rs17185181	0.83[AFR][1000 genomes]
rs17185293	0.88[AFR][1000 genomes]
rs17185314	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs17185342	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17185363	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17185398	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17875389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17875391	0.83[AFR][1000 genomes]
rs17875393	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17875395	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17875396	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28372986	0.83[AFR][1000 genomes]
rs28397055	0.83[AFR][1000 genomes]
rs28579685	0.83[AFR][1000 genomes]
rs28634576	0.83[AFR][1000 genomes]
rs3888577	0.93[AFR][1000 genomes]
rs56813912	0.93[AFR][1000 genomes]
rs57146053	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57541649	0.93[AFR][1000 genomes]
rs57644190	0.87[EUR][1000 genomes]
rs58552394	0.93[AFR][1000 genomes]
rs59508891	0.83[AFR][1000 genomes]
rs61276793	0.93[AFR][1000 genomes]
rs61580820	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61729757	0.83[AFR][1000 genomes]
rs61737605	0.83[AFR][1000 genomes]
rs7755504	0.87[EUR][1000 genomes]
rs7765248	0.83[AFR][1000 genomes]
rs9295815	0.83[AFR][1000 genomes]
rs9295816	0.83[AFR][1000 genomes]
rs9295817	0.83[AFR][1000 genomes]
rs9295818	0.83[AFR][1000 genomes]
rs9461559	0.83[AFR][1000 genomes]
rs9461562	0.86[AFR][1000 genomes]
rs9461563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468610	0.83[AFR][1000 genomes]
rs9468611	0.83[AFR][1000 genomes]
rs9468612	0.83[AFR][1000 genomes]
rs9468613	0.83[AFR][1000 genomes]
rs9468622	0.81[AFR][1000 genomes]
rs9468623	0.81[AFR][1000 genomes]
rs9468624	0.83[AFR][1000 genomes]
rs9468626	0.83[AFR][1000 genomes]
rs9468627	0.83[AFR][1000 genomes]
rs9468629	0.83[AFR][1000 genomes]
rs9468630	0.83[AFR][1000 genomes]
rs9468632	0.83[AFR][1000 genomes]
rs9468638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9500846	0.83[AFR][1000 genomes]
rs9500851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9500987	0.83[AFR][1000 genomes]
rs9500988	0.90[AFR][1000 genomes]
rs9500990	0.83[AFR][1000 genomes]
rs9500995	0.88[AFR][1000 genomes]
rs9500997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9500998	0.83[AFR][1000 genomes]
rs9501416	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9501417	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv883532	chr6:29703262-29814963	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv3441842	chr6:29715749-29942950	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	esv11180	chr6:29729381-29800066	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv3332677	chr6:29733187-29961463	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	esv3423001	chr6:29733216-29878601	Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	esv3475027	chr6:29733297-29922699	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	esv3475028	chr6:29733297-29922699	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	esv3420260	chr6:29734457-29835593	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	esv3330285	chr6:29736281-29881328	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
13	esv3396224	chr6:29754243-29888093	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
14	nsv965702	chr6:29758408-29798943	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	esv3430372	chr6:29759523-29974277	Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
16	esv3426050	chr6:29761594-29918407	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
17	esv3431350	chr6:29765473-29922767	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
18	esv3354193	chr6:29773857-29867902	Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
19	esv3451016	chr6:29774115-29929436	Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
20	esv3369144	chr6:29775824-29872385	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
21	esv3500392	chr6:29777854-29871802	Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
22	esv3500393	chr6:29777854-29871802	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
23	esv3384912	chr6:29778488-29872579	ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
24	esv3431922	chr6:29779132-29873171	Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
25	esv3338581	chr6:29780045-29890754	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
26	esv17468	chr6:29782014-29923275	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
27	esv3411103	chr6:29783090-29930409	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
28	esv2758040	chr6:29792434-29975144	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
29	esv2759412	chr6:29792434-29975144	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
30	esv20324	chr6:29793378-29832922	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29794600-29796600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:29795200-29796600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:29795200-29796600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:29795200-29796600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:29795200-29796600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:29795200-29796800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr6:29795200-29797000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:29795400-29796400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
9	chr6:29795400-29796400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:29795400-29796400	Bivalent Enhancer	Small Intestine	intestine
11	chr6:29795400-29796600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr6:29795400-29796600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:29795400-29796600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr6:29795400-29796600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
15	chr6:29795400-29796800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
16	chr6:29795400-29796800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:29795400-29796800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
18	chr6:29795400-29796800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
19	chr6:29795400-29796800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:29795400-29796800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:29795400-29796800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
22	chr6:29795400-29796800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
23	chr6:29795600-29796400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:29795600-29796400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
25	chr6:29795600-29796400	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:29795600-29796400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:29795600-29796400	Bivalent Enhancer	Fetal Brain Male	brain
28	chr6:29795600-29796400	Bivalent Enhancer	Fetal Stomach	stomach
29	chr6:29795600-29796400	Flanking Active TSS	Right Ventricle	heart
30	chr6:29795600-29796400	Bivalent Enhancer	Stomach Mucosa	stomach
31	chr6:29795600-29796600	Bivalent Enhancer	Primary B cells from cord blood	blood
32	chr6:29795600-29796600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
33	chr6:29795600-29796600	Bivalent Enhancer	Fetal Heart	heart
34	chr6:29795600-29796600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
35	chr6:29795600-29796600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
36	chr6:29795600-29796600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
37	chr6:29795600-29796800	Bivalent/Poised TSS	Primary T helper naive cells from peripheral blood	blood
38	chr6:29795600-29796800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:29795600-29796800	Enhancers	Lung	lung
40	chr6:29795600-29796800	Active TSS	Hela-S3	cervix
41	chr6:29795600-29796800	Bivalent/Poised TSS	NHDF-Ad	bronchial
42	chr6:29795600-29796800	Bivalent/Poised TSS	NHEK	skin
43	chr6:29795800-29796400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:29795800-29796400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
45	chr6:29795800-29796400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
46	chr6:29795800-29796400	Active TSS	Right Atrium	heart
47	chr6:29795800-29796600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
48	chr6:29795800-29796600	Flanking Active TSS	Pancreas	Pancrea
49	chr6:29795800-29796800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
50	chr6:29795800-29796800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood

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