Variant report

Variant	rs11924939
Chromosome Location	chr3:138665796-138665797
allele	C/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	ZBTB7A	chr3:138665318-138666608	K562	blood:	n/a	n/a
2	POLR2A	chr3:138664948-138666357	Hela-S3	cervix:	n/a	n/a
3	RCOR1	chr3:138665624-138666322	K562	blood:	n/a	n/a
4	SMARCB1	chr3:138664989-138666842	Hela-S3	cervix:	n/a	n/a
5	MAZ	chr3:138665017-138666795	K562	blood:	n/a	chr3:138666114-138666124
6	CREB1	chr3:138665770-138666184	A549	lung:	n/a	n/a
7	MXI1	chr3:138665772-138666228	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr3:138665657-138666249	H1-hESC	embryonic stem cell:	n/a	n/a
9	YY1	chr3:138664704-138666204	K562	blood:	n/a	chr3:138664897-138664917 chr3:138666106-138666117 chr3:138665889-138665898
10	CHD1	chr3:138665620-138665820	H1-hESC	embryonic stem cell:	n/a	n/a
11	ELF1	chr3:138665755-138666229	K562	blood:	n/a	n/a
12	TAF1	chr3:138664973-138666613	K562	blood:	n/a	n/a
13	MAX	chr3:138665570-138666469	H1-hESC	embryonic stem cell:	n/a	chr3:138666114-138666124
14	POLR2A	chr3:138664890-138666825	K562	blood:	n/a	n/a
15	POLR2A	chr3:138665748-138666299	A549	lung:	n/a	n/a
16	TBP	chr3:138665785-138666250	Hela-S3	cervix:	n/a	n/a
17	HCFC1	chr3:138664826-138666363	Hela-S3	cervix:	n/a	n/a
18	SIN3A	chr3:138665532-138666575	H1-hESC	embryonic stem cell:	n/a	chr3:138665612-138665625 chr3:138666039-138666050 chr3:138665609-138665618
19	HEY1	chr3:138665462-138666614	K562	blood:	n/a	chr3:138665812-138665827
20	TCF7L2	chr3:138665788-138666220	Hela-S3	cervix:	n/a	n/a
21	TBP	chr3:138664919-138666740	K562	blood:	n/a	n/a
22	E2F4	chr3:138664772-138666227	K562	blood:	n/a	chr3:138666110-138666120 chr3:138665889-138665898
23	MAX	chr3:138664549-138666373	A549	lung:	n/a	chr3:138666114-138666124
24	MAX	chr3:138663821-138666675	K562	blood:	n/a	chr3:138666114-138666124
25	E2F6	chr3:138663661-138666655	H1-hESC	embryonic stem cell:	n/a	chr3:138666110-138666120 chr3:138665889-138665898
26	POLR2A	chr3:138665082-138666478	K562	blood:	n/a	n/a
27	BRCA1	chr3:138665645-138665802	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr3:138665748-138666341	PANC-1	pancreas:	n/a	n/a
29	RCOR1	chr3:138665037-138666727	K562	blood:	n/a	n/a
30	YY1	chr3:138665508-138665856	H1-hESC	embryonic stem cell:	n/a	n/a
31	TEAD4	chr3:138665637-138666328	K562	blood:	n/a	n/a
32	ZMIZ1	chr3:138665776-138666186	K562	blood:	n/a	n/a
33	UBTF	chr3:138664715-138666727	K562	blood:	n/a	n/a
34	ZNF143	chr3:138665542-138665860	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr3:138665608-138666744	Hela-S3	cervix:	n/a	n/a
36	IRF1	chr3:138665727-138666221	K562	blood:	n/a	chr3:138665885-138665899
37	MYC	chr3:138665617-138666775	K562	blood:	n/a	chr3:138666114-138666124
38	YY1	chr3:138665459-138666022	H1-hESC	embryonic stem cell:	n/a	chr3:138665889-138665898
39	POLR2A	chr3:138664719-138666765	K562	blood:	n/a	n/a
40	POLR2A	chr3:138665645-138666508	K562	blood:	n/a	n/a
41	ELF1	chr3:138665424-138666248	K562	blood:	n/a	n/a
42	IRF1	chr3:138665790-138666177	K562	blood:	n/a	chr3:138665885-138665899
43	POLR2A	chr3:138665481-138666294	Hela-S3	cervix:	n/a	n/a
44	ZC3H11A	chr3:138665758-138665823	K562	blood:	n/a	n/a
45	CCNT2	chr3:138663704-138666364	K562	blood:	n/a	chr3:138665889-138665898 chr3:138665882-138665891
46	GTF2F1	chr3:138665613-138666271	K562	blood:	n/a	n/a
47	MAX	chr3:138663637-138666899	K562	blood:	n/a	chr3:138666114-138666124
48	E2F6	chr3:138665716-138666169	A549	lung:	n/a	chr3:138666110-138666120 chr3:138665889-138665898
49	YY1	chr3:138664945-138666307	K562	blood:	n/a	chr3:138666106-138666117 chr3:138665889-138665898
50	E2F6	chr3:138663622-138666590	K562	blood:	n/a	chr3:138666110-138666120 chr3:138665889-138665898

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138552263..138555163-chr3:138665790..138667540,3	K562	blood:

Variant related genes	Relation type
C3orf72	TF binding region
ENSG00000244578	TF binding region
ENSG00000051382	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11708762	1.00[CHB][hapmap]
rs12631035	1.00[CHB][hapmap]
rs13080973	1.00[CHB][hapmap]
rs17485052	1.00[CHB][hapmap]
rs4894359	1.00[CHB][hapmap]
rs6773514	1.00[CHB][hapmap]
rs7613579	1.00[CHB][hapmap]
rs7650967	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv877540	chr3:138645013-138670695	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv877541	chr3:138645013-138673922	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv877542	chr3:138645013-138750904	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	esv3338518	chr3:138663787-138666635	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv529311	chr3:138665250-138667190	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138662400-138666600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:138662800-138666600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr3:138663000-138666400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr3:138663000-138666600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:138663000-138666600	Active TSS	Hela-S3	cervix
6	chr3:138663200-138666000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
7	chr3:138663200-138666000	Bivalent Enhancer	Small Intestine	intestine
8	chr3:138663400-138666400	Bivalent Enhancer	Fetal Brain Male	brain
9	chr3:138663400-138666600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr3:138663600-138666400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:138663600-138666600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr3:138663600-138666600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
13	chr3:138663600-138666800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr3:138663800-138665800	Flanking Bivalent TSS/Enh	Right Ventricle	heart
15	chr3:138663800-138666200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
16	chr3:138663800-138666400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:138663800-138666400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:138663800-138666400	Bivalent/Poised TSS	Psoas Muscle	Psoas
19	chr3:138664000-138666200	Bivalent/Poised TSS	HSMM	muscle
20	chr3:138664200-138665800	Enhancers	Gastric	stomach
21	chr3:138664200-138666400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:138664200-138666600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:138664400-138666000	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr3:138664400-138666400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:138664400-138666600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:138664400-138666600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
27	chr3:138664400-138666800	Active TSS	NHDF-Ad	bronchial
28	chr3:138664600-138665800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
29	chr3:138664600-138666000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
30	chr3:138664600-138666400	Active TSS	Aorta	Aorta
31	chr3:138664600-138666600	Active TSS	K562	blood
32	chr3:138664600-138668800	Active TSS	Ovary	ovary
33	chr3:138664800-138665800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
34	chr3:138664800-138665800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:138664800-138665800	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
36	chr3:138664800-138666000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
37	chr3:138664800-138666000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
38	chr3:138664800-138666200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:138664800-138666200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
40	chr3:138664800-138666200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
41	chr3:138664800-138666200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
42	chr3:138664800-138666200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:138664800-138666200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
44	chr3:138664800-138666200	Flanking Active TSS	Pancreas	Pancrea
45	chr3:138664800-138666400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:138664800-138666400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:138664800-138666400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:138664800-138666400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
49	chr3:138664800-138666400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:138664800-138666400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain

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