Variant report

Variant	rs1997164
Chromosome Location	chr7:102068619-102068620
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	POLR2A	chr7:102064052-102068639	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:102067757-102068845	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:102064166-102068636	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:102065043..102072034-chr7:102072127..102076587,12	MCF-7	breast:
2	chr7:102063400..102066927-chr7:102067037..102070121,4	K562	blood:

Variant related genes	Relation type
ORAI2	TF binding region
ENSG00000160991	Chromatin interaction
ENSG00000239480	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10225683	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10226565	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10233236	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10233461	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10235407	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10237343	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10239657	0.82[EUR][1000 genomes]
rs10243209	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10246324	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10249217	0.84[EUR][1000 genomes]
rs10249222	0.84[EUR][1000 genomes]
rs10249581	0.82[EUR][1000 genomes]
rs10255036	0.82[EUR][1000 genomes]
rs10268289	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10268970	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10276094	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10277996	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10278274	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1131384	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs11982980	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11983129	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12672132	0.81[EUR][1000 genomes]
rs1293832	0.86[AMR][1000 genomes]
rs17135197	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1983476	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2103229	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2410990	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2411005	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28427402	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28539797	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28879187	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4481505	0.85[GIH][hapmap]
rs4729789	0.85[GIH][hapmap]
rs56295031	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6465859	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6947435	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6951185	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6953087	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6958795	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6968325	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6970496	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6974177	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7384178	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7385200	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7787493	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1814780	chr7:101912320-102375950	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv1819566	chr7:101912320-102375950	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1822347	chr7:101912320-102375950	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	esv1825708	chr7:101912320-102375950	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	esv1842898	chr7:101912320-102375950	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	esv1847418	chr7:101912320-102375950	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
7	nsv427798	chr7:101912320-102375950	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv428182	chr7:101912320-102375950	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
10	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
11	nsv1029079	chr7:101939998-102112371	Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active 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	32 gene(s)	inside rSNPs	diseases
12	esv1818954	chr7:101957513-102328097	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	esv1828190	chr7:101966669-102439077	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
14	esv1829377	chr7:101970299-102330884	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv831083	chr7:101981005-102295869	Active TSS Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
16	esv1806297	chr7:101981544-102330884	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
17	esv1810415	chr7:101993063-102375950	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
18	esv1811751	chr7:101993063-102375950	Enhancers Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
19	esv1829118	chr7:101993063-102375950	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers 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 lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
20	esv1833155	chr7:101993063-102375950	Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1997164	ORAI2	cis	Whole Blood	GTEx
rs1997164	AGFG2	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102039200-102070000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr7:102050800-102073400	Weak transcription	Psoas Muscle	Psoas
3	chr7:102051200-102073400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr7:102051400-102074400	Weak transcription	Fetal Heart	heart
5	chr7:102051600-102070000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:102053600-102073200	Weak transcription	Right Atrium	heart
7	chr7:102054000-102073400	Weak transcription	Small Intestine	intestine
8	chr7:102061600-102071400	Weak transcription	Fetal Kidney	kidney
9	chr7:102061600-102072200	Weak transcription	HMEC	breast
10	chr7:102063400-102071000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:102064000-102068800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:102064600-102068800	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr7:102065000-102069200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr7:102065400-102071000	Weak transcription	Fetal Brain Male	brain
15	chr7:102065600-102068800	Strong transcription	HSMM	muscle
16	chr7:102065600-102071200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr7:102066000-102073400	Weak transcription	HUVEC	blood vessel
18	chr7:102066200-102069200	Strong transcription	Fetal Stomach	stomach
19	chr7:102066200-102071200	Weak transcription	K562	blood
20	chr7:102066200-102072400	Weak transcription	Brain Angular Gyrus	brain
21	chr7:102066200-102074000	Weak transcription	Fetal Lung	lung
22	chr7:102066400-102069200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:102066400-102072200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr7:102066400-102073600	Weak transcription	NHDF-Ad	bronchial
25	chr7:102066600-102071200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr7:102066600-102073400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr7:102066800-102069800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr7:102066800-102069800	Strong transcription	Fetal Intestine Small	intestine
29	chr7:102066800-102070000	Weak transcription	Esophagus	oesophagus
30	chr7:102066800-102073200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr7:102067000-102071400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr7:102067000-102072200	Weak transcription	Colon Smooth Muscle	Colon
33	chr7:102067200-102071200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr7:102067400-102071400	Weak transcription	A549	lung
35	chr7:102067400-102073200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:102067400-102073200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:102067400-102073400	Weak transcription	Aorta	Aorta
38	chr7:102067400-102073400	Weak transcription	NH-A	brain
39	chr7:102067400-102073600	Weak transcription	Hela-S3	cervix
40	chr7:102067600-102069000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr7:102067600-102069800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr7:102067600-102069800	Genic enhancers	Fetal Thymus	thymus
43	chr7:102067600-102070200	Strong transcription	Fetal Muscle Leg	muscle
44	chr7:102067600-102070400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr7:102067600-102071400	Enhancers	Primary T cells fromperipheralblood	blood
46	chr7:102067600-102071400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr7:102067600-102071600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr7:102067600-102071800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr7:102067600-102072000	Enhancers	Primary B cells from peripheral blood	blood
50	chr7:102067600-102072000	Enhancers	Primary T helper cells fromperipheralblood	blood

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