Variant report

Variant	rs372989
Chromosome Location	chr7:101714581-101714582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10268506	1.00[CHB][hapmap]
rs365397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs366345	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.80[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs367773	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs370760	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372321	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs375417	0.87[CEU][hapmap]
rs376183	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs377587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377612	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs379347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380934	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs402294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs406012	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs409420	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs411844	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs412332	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs412524	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413348	1.00[ASN][1000 genomes]
rs420709	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs421154	1.00[ASN][1000 genomes]
rs421430	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425577	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4294126	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs430154	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432002	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432600	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438908	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs441160	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443159	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443293	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4729771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73185898	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482521	chr7:101604002-101718950	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv831080	chr7:101629121-101718950	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1027574	chr7:101654060-101718950	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv607985	chr7:101683563-101718950	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs372989	BRI3	cis	cerebellum	SCAN
rs372989	CUX1	cis	cerebellum	SCAN
rs372989	C7orf59	cis	parietal	SCAN
rs372989	ZKSCAN5	cis	parietal	SCAN
rs372989	TRIP6	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101689400-101714600	Weak transcription	HSMMtube	muscle
2	chr7:101689800-101714800	Weak transcription	NHLF	lung
3	chr7:101705600-101714800	Weak transcription	Fetal Kidney	kidney
4	chr7:101705600-101717400	Weak transcription	Pancreas	Pancrea
5	chr7:101707200-101738000	Weak transcription	Colon Smooth Muscle	Colon
6	chr7:101707400-101715800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr7:101707600-101714600	Weak transcription	Osteobl	bone
8	chr7:101707600-101716400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:101708000-101714800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:101708000-101715000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr7:101708000-101722800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr7:101708200-101714600	Weak transcription	Colonic Mucosa	Colon
13	chr7:101708200-101714600	Weak transcription	Esophagus	oesophagus
14	chr7:101708200-101722000	Weak transcription	NH-A	brain
15	chr7:101708200-101723000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr7:101708200-101765000	Weak transcription	Small Intestine	intestine
17	chr7:101708400-101714600	Weak transcription	Fetal Brain Female	brain
18	chr7:101708400-101720400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr7:101708400-101720400	Weak transcription	HMEC	breast
20	chr7:101708400-101722800	Weak transcription	Brain Substantia Nigra	brain
21	chr7:101708400-101722800	Weak transcription	Right Atrium	heart
22	chr7:101708400-101726000	Weak transcription	NHEK	skin
23	chr7:101708600-101714600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr7:101708600-101714600	Weak transcription	A549	lung
25	chr7:101708800-101714600	Weak transcription	Brain Germinal Matrix	brain
26	chr7:101709400-101720000	Strong transcription	Fetal Stomach	stomach
27	chr7:101709600-101715200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr7:101710400-101715200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr7:101711000-101723200	Weak transcription	Brain Angular Gyrus	brain
30	chr7:101711600-101714800	Strong transcription	Spleen	Spleen
31	chr7:101711800-101714800	Strong transcription	Stomach Smooth Muscle	stomach
32	chr7:101711800-101714800	Strong transcription	Dnd41	blood
33	chr7:101711800-101715800	Strong transcription	Liver	Liver
34	chr7:101711800-101717000	Strong transcription	HepG2	liver
35	chr7:101712000-101714600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr7:101712000-101714600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr7:101712000-101714800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:101712000-101714800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr7:101712000-101715200	Strong transcription	Primary T cells from cord blood	blood
40	chr7:101712000-101715800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr7:101712000-101716000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr7:101712000-101716000	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr7:101712000-101718000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:101712000-101719600	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr7:101712200-101714600	Strong transcription	Fetal Muscle Leg	muscle
46	chr7:101712200-101714800	Strong transcription	Adipose Nuclei	Adipose
47	chr7:101712200-101716000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr7:101712400-101714800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr7:101712400-101715200	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr7:101712400-101718800	Strong transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links