Variant report

Variant	rs6697910
Chromosome Location	chr1:212586836-212586837
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	ZNF263	chr1:212586794-212588562	HEK293-T-REx	kidney:	n/a	chr1:212587473-212587482 chr1:212587663-212587672
2	JUN	chr1:212586575-212589515	K562	blood:	n/a	chr1:212587985-212587994 chr1:212589466-212589475
3	MXI1	chr1:212586634-212588790	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:212458597..212460542-chr1:212586367..212588357,2	MCF-7	breast:
2	chr1:212550848..212553114-chr1:212586010..212588532,2	MCF-7	breast:
3	chr1:212586222..212588940-chr1:212781343..212783037,2	K562	blood:
4	chr1:212586060..212592297-chr1:212603893..212609565,9	MCF-7	breast:
5	chr1:212457988..212460167-chr1:212585002..212587734,2	MCF-7	breast:
6	chr1:212549233..212551182-chr1:212586836..212589324,2	K562	blood:
7	chr1:212585974..212594847-chr1:212598812..212609579,19	K562	blood:
8	chr1:212586665..212588349-chr1:212964322..212966191,2	MCF-7	breast:
9	chr1:212581574..212584496-chr1:212586803..212589409,2	MCF-7	breast:

Variant related genes	Relation type
TMEM206	TF binding region
ENSG00000117697	Chromatin interaction
ENSG00000203705	Chromatin interaction
ENSG00000066027	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000065600	Chromatin interaction
ENSG00000117691	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10494951	0.81[TSI][hapmap]
rs11590242	0.81[TSI][hapmap]
rs11803766	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12739715	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12755383	0.99[EUR][1000 genomes]
rs17018997	1.00[CEU][hapmap];0.85[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2120770	0.84[TSI][hapmap]
rs35702733	0.98[EUR][1000 genomes]
rs35822123	0.82[EUR][1000 genomes]
rs4336916	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4540733	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6666415	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6669027	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6676208	1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs6693849	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6704234	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71646158	0.82[EUR][1000 genomes]
rs71646159	0.93[EUR][1000 genomes]
rs71646161	0.99[EUR][1000 genomes]
rs7518399	0.83[TSI][hapmap]
rs7533689	0.82[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7551910	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	esv1828436	chr1:212577765-212591863	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6697910	LOC148696	cis	parietal	SCAN
rs6697910	ATF3	cis	parietal	SCAN
rs6697910	BATF3	cis	cerebellum	SCAN
rs6697910	RP11-15I11.3	cis	lung	GTEx
rs6697910	RP11-15I11.3	cis	Thyroid	GTEx
rs6697910	C1orf74	cis	parietal	SCAN
rs6697910	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212556800-212587600	Weak transcription	Small Intestine	intestine
2	chr1:212579800-212587000	Weak transcription	Right Atrium	heart
3	chr1:212580600-212587200	Weak transcription	HSMMtube	muscle
4	chr1:212580800-212587000	Weak transcription	NHDF-Ad	bronchial
5	chr1:212583200-212587000	Weak transcription	Fetal Heart	heart
6	chr1:212583200-212587000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:212583600-212587000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr1:212583600-212587000	Weak transcription	Hela-S3	cervix
9	chr1:212583800-212587000	Weak transcription	Right Ventricle	heart
10	chr1:212583800-212587000	Weak transcription	A549	lung
11	chr1:212583800-212587000	Weak transcription	NH-A	brain
12	chr1:212584000-212587000	Weak transcription	Fetal Kidney	kidney
13	chr1:212584000-212587200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:212584000-212587400	Weak transcription	Ovary	ovary
15	chr1:212584200-212587000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:212584200-212587000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:212584200-212587000	Weak transcription	NHLF	lung
18	chr1:212584200-212587200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:212584200-212587200	Weak transcription	Fetal Lung	lung
20	chr1:212584200-212587200	Weak transcription	Osteobl	bone
21	chr1:212584400-212587000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:212584400-212587000	Weak transcription	Liver	Liver
23	chr1:212584400-212587000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:212584400-212587200	Weak transcription	Fetal Intestine Large	intestine
25	chr1:212584400-212587200	Weak transcription	Gastric	stomach
26	chr1:212584600-212587200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:212584800-212587000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:212584800-212587000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:212584800-212587000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:212584800-212587000	Weak transcription	Left Ventricle	heart
31	chr1:212584800-212587200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:212585000-212587000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:212585000-212587000	Weak transcription	HSMM	muscle
34	chr1:212585000-212587400	Weak transcription	Aorta	Aorta
35	chr1:212585200-212587000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:212585600-212587000	Enhancers	HepG2	liver
37	chr1:212585600-212587200	Enhancers	Primary B cells from peripheral blood	blood
38	chr1:212585600-212587200	Enhancers	Primary T cells fromperipheralblood	blood
39	chr1:212585600-212587200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr1:212585800-212587000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:212585800-212587200	Enhancers	Primary B cells from cord blood	blood
42	chr1:212585800-212587400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:212585800-212587400	Flanking Active TSS	GM12878-XiMat	blood
44	chr1:212586000-212587000	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr1:212586000-212587000	Enhancers	Fetal Muscle Leg	muscle
46	chr1:212586000-212587200	Genic enhancers	Fetal Thymus	thymus
47	chr1:212586000-212587200	Genic enhancers	K562	blood
48	chr1:212586000-212587600	Flanking Active TSS	Dnd41	blood
49	chr1:212586200-212587000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:212586200-212587000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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