Variant report

Variant	rs9258241
Chromosome Location	chr6:29715857-29715858
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr6:29715850-29716823	HEK293-T-REx	kidney:	n/a	chr6:29716015-29716036 chr6:29715958-29715967 chr6:29716063-29716084
2	RCOR1	chr6:29715680-29715880	HepG2	liver:	n/a	n/a
3	SIN3A	chr6:29715713-29717573	H1-hESC	embryonic stem cell:	n/a	chr6:29717251-29717262 chr6:29717074-29717085
4	POLR2A	chr6:29715691-29717474	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29715846-29715896	GM12878	blood:	n/a
2	chr6:29715846-29715896	MCF-7	breast:	n/a
3	chr6:29715846-29715896	IMR90	lung:	fetal
4	chr6:29715846-29715896	HRE	kidney:	n/a
5	chr6:29715846-29715896	HL-60	blood:	n/a
6	chr6:29715846-29715896	HIPEpiC	eye:	n/a
7	chr6:29715846-29715896	ProgFib	skin:	n/a
8	chr6:29715846-29715896	ECC-1	luminal epithelium:	n/a
9	chr6:29715846-29715896	AG10803	skin:	n/a
10	chr6:29715846-29715896	HRCEpiC	kidney:	n/a
11	chr6:29715846-29715896	Caco-2	colon:	n/a
12	chr6:29715846-29715896	T-47D	breast:	n/a
13	chr6:29715846-29715896	HCPEpiC	choroid plexus:	n/a
14	chr6:29715846-29715896	GM12892	blood:	n/a
15	chr6:29715846-29715896	H1-hESC	embryonic stem cell:	embryo
16	chr6:29715846-29715896	HCT-116	colon:	n/a
17	chr6:29715846-29715896	SK-N-SH	brain:	n/a
18	chr6:29715846-29715896	NHDF-neo	bronchial:	n/a
19	chr6:29715846-29715896	HAEpiC	amniotic membrane:	n/a
20	chr6:29715846-29715896	BJ	skin:	n/a
21	chr6:29715846-29715896	Hepatocyte	liver:	n/a
22	chr6:29715846-29715896	NT2-D1	testis:	n/a
23	chr6:29715846-29715896	AG09319	gingival:	n/a
24	chr6:29715846-29715896	SK-N-MC	brain:	n/a
25	chr6:29715846-29715896	HepG2	liver:	n/a
26	chr6:29715846-29715896	HUVEC	blood vessel:	n/a
27	chr6:29715846-29715896	HEK293	kidney:	embryo
28	chr6:29715846-29715896	HMEC	breast:	n/a
29	chr6:29715846-29715896	AG04450	lung:	fetal
30	chr6:29715846-29715896	GM19239	blood:	n/a
31	chr6:29715846-29715896	AoSMC	blood vessel:	n/a
32	chr6:29715846-29715896	PANC-1	pancreas:	n/a
33	chr6:29715846-29715896	HNPCEpiC	eye:	n/a
34	chr6:29715846-29715896	SAEC	small airway:	n/a
35	chr6:29715846-29715896	GM06990	blood:	n/a
36	chr6:29715846-29715896	ovcar-3	ovarian:	n/a
37	chr6:29715846-29715896	HEEpiC	esophagus:	n/a
38	chr6:29715846-29715896	NHBE	bronchial:	n/a
39	chr6:29715846-29715896	LNCaP	prostate:	n/a
40	chr6:29715846-29715896	U87	brain:	n/a
41	chr6:29715846-29715896	AG04449	skin:	fetal
42	chr6:29715846-29715896	SKMC	muscle:	n/a
43	chr6:29715846-29715896	HRPEpiC	eye:	n/a
44	chr6:29715846-29715896	GM12891	blood:	n/a
45	chr6:29715846-29715896	PFSK-1	brain:	n/a
46	chr6:29715846-29715896	NB4	blood:	n/a
47	chr6:29715846-29715896	PrEC	prostate:	n/a
48	chr6:29715846-29715896	RPTEC	kidney:	n/a
49	chr6:29715846-29715896	MCF10A-Er-Src	breast:	n/a
50	chr6:29715846-29715896	Hela-S3	cervix:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29713370..29715869-chr6:29729277..29731286,2	MCF-7	breast:

No data

Variant related genes	Relation type
HCG9P5	TF binding region
ENSG00000199290	TF binding region
ENSG00000199290	CpG island
HCG9P5	CpG island
ENSG00000270896	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1633066	0.84[ASN][1000 genomes]
rs1736913	0.82[ASN][1000 genomes]
rs1736919	0.81[ASN][1000 genomes]
rs1737069	0.84[ASN][1000 genomes]
rs2072894	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072896	0.91[ASN][1000 genomes]
rs2075682	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2076174	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272874	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3734813	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3734815	0.91[ASN][1000 genomes]
rs3736694	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3736697	0.91[ASN][1000 genomes]
rs3757324	0.90[ASN][1000 genomes]
rs3757325	0.90[ASN][1000 genomes]
rs3757326	0.90[ASN][1000 genomes]
rs3817826	0.88[ASN][1000 genomes]
rs3823318	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6901686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6910733	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7739360	0.81[ASN][1000 genomes]
rs7739388	0.81[ASN][1000 genomes]
rs7741597	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7742523	0.91[ASN][1000 genomes]
rs7751815	0.98[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7753946	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7754692	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7755571	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7759272	0.81[ASN][1000 genomes]
rs7773358	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9258156	0.81[ASN][1000 genomes]
rs9258158	0.89[ASN][1000 genomes]
rs9258160	0.89[ASN][1000 genomes]
rs9258163	0.90[ASN][1000 genomes]
rs9258164	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9258166	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9258167	0.90[ASN][1000 genomes]
rs9258168	0.90[ASN][1000 genomes]
rs9258169	0.90[ASN][1000 genomes]
rs9258170	0.90[ASN][1000 genomes]
rs9258171	0.90[ASN][1000 genomes]
rs9258172	0.90[ASN][1000 genomes]
rs9258173	0.90[ASN][1000 genomes]
rs9258174	0.90[ASN][1000 genomes]
rs9258175	0.90[ASN][1000 genomes]
rs9258187	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9258192	0.91[ASN][1000 genomes]
rs9258203	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258205	0.98[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9258207	0.98[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9258211	0.98[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9258212	0.98[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9258214	0.98[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9258215	0.98[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9258216	0.95[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9258218	0.98[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9258222	0.89[AFR][1000 genomes]
rs9258223	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9258224	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258225	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9258226	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9258227	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9258228	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9258229	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9258230	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9258236	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9258242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9258244	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258258	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258259	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258260	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258262	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258265	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258272	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9258274	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised 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	28 gene(s)	inside rSNPs	diseases
8	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	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
10	nsv883533	chr6:29704237-29715997	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv883534	chr6:29708222-29724310	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	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

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29693800-29716000	Weak transcription	Small Intestine	intestine
2	chr6:29712800-29716000	Weak transcription	Aorta	Aorta
3	chr6:29715200-29717200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:29715400-29716000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:29715400-29716000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:29715400-29716000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
7	chr6:29715400-29716000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
8	chr6:29715400-29716000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:29715400-29716000	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr6:29715400-29716200	Flanking Active TSS	Hela-S3	cervix
11	chr6:29715400-29717400	Active TSS	H9 Cell Line	embryonic stem cell
12	chr6:29715400-29717600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr6:29715400-29717800	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr6:29715600-29716000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:29715600-29716000	Enhancers	Primary B cells from peripheral blood	blood
16	chr6:29715600-29716000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:29715600-29716000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:29715600-29716000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:29715600-29716000	Enhancers	Liver	Liver
20	chr6:29715600-29716000	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr6:29715600-29716000	Enhancers	Esophagus	oesophagus
22	chr6:29715600-29716000	Bivalent Enhancer	Fetal Heart	heart
23	chr6:29715600-29716000	Bivalent Enhancer	Placenta	Placenta
24	chr6:29715600-29716200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:29715600-29716200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
26	chr6:29715600-29716200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
27	chr6:29715600-29716200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr6:29715600-29716200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr6:29715600-29716200	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr6:29715600-29716200	Flanking Active TSS	Right Ventricle	heart
31	chr6:29715600-29716200	Flanking Active TSS	NHEK	skin
32	chr6:29715600-29716400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:29715600-29716400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:29715600-29716400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:29715600-29716400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:29715600-29716400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
37	chr6:29715600-29716600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr6:29715600-29716800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr6:29715600-29716800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr6:29715600-29716800	Flanking Bivalent TSS/Enh	HepG2	liver
41	chr6:29715600-29717200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
42	chr6:29715600-29717200	Active TSS	Rectal Smooth Muscle	rectum
43	chr6:29715600-29717400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr6:29715600-29718000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
45	chr6:29715800-29716000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
46	chr6:29715800-29716000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:29715800-29716000	Enhancers	Primary B cells from cord blood	blood
48	chr6:29715800-29716000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
49	chr6:29715800-29716000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:29715800-29716000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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