Variant report

Variant	rs2968854
Chromosome Location	chr7:150637834-150637835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10236214	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap]
rs10378	1.00[JPT][hapmap]
rs1547958	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17197782	1.00[JPT][hapmap]
rs1800779	0.85[GIH][hapmap]
rs1805123	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2907948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968863	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968864	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34775896	1.00[JPT][hapmap]
rs3807370	0.88[GIH][hapmap]
rs4496877	0.88[GIH][hapmap]
rs4725386	0.86[EUR][1000 genomes]
rs4725984	1.00[CHB][hapmap]
rs56282717	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6947240	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6951150	0.88[GIH][hapmap]

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	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv2758140	chr7:150538821-150663697	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2759574	chr7:150538821-150663697	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv1821419	chr7:150593315-150974269	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
8	nsv465212	chr7:150598492-150667210	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv609000	chr7:150598492-150667210	Genic enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv465213	chr7:150606288-150667210	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv609001	chr7:150606288-150667210	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
12	nsv1022246	chr7:150619660-150779924	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2968854	ZNF777	cis	parietal	SCAN
rs2968854	ZNF862	cis	cerebellum	SCAN
rs2968854	CNTNAP2	cis	parietal	SCAN
rs2968854	KCNH2	cis	cerebellum	SCAN
rs2968854	ASB10	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150634400-150640400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr7:150634400-150643800	Enhancers	HMEC	breast
3	chr7:150634600-150638000	Enhancers	Fetal Stomach	stomach
4	chr7:150634800-150643600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:150635000-150644400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr7:150635600-150638400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr7:150635600-150639200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:150635600-150642400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:150635600-150642600	Weak transcription	Brain Anterior Caudate	brain
10	chr7:150635600-150648000	Weak transcription	Ovary	ovary
11	chr7:150635800-150638600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:150635800-150638800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:150635800-150639000	Weak transcription	Right Atrium	heart
14	chr7:150635800-150639000	Weak transcription	Right Ventricle	heart
15	chr7:150635800-150639200	Weak transcription	Spleen	Spleen
16	chr7:150636000-150638600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr7:150636000-150638600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr7:150636000-150638600	Weak transcription	Esophagus	oesophagus
19	chr7:150636000-150638800	Weak transcription	Colon Smooth Muscle	Colon
20	chr7:150636000-150639200	Weak transcription	Primary T cells from cord blood	blood
21	chr7:150636000-150639200	Weak transcription	Fetal Lung	lung
22	chr7:150636400-150638000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr7:150636400-150638600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr7:150636400-150638600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr7:150636400-150638600	Weak transcription	NHEK	skin
26	chr7:150636600-150638600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr7:150636600-150638600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr7:150636600-150638600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr7:150636600-150638600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr7:150636800-150638400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr7:150636800-150638600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr7:150636800-150638800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr7:150636800-150639000	Weak transcription	Fetal Brain Male	brain
34	chr7:150636800-150639000	Weak transcription	K562	blood
35	chr7:150637000-150638600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr7:150637000-150638600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr7:150637000-150639000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr7:150637000-150642000	Weak transcription	Fetal Brain Female	brain
39	chr7:150637200-150638400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:150637200-150641200	Enhancers	Fetal Heart	heart
41	chr7:150637400-150638000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:150637800-150638000	Enhancers	Fetal Intestine Small	intestine
43	chr7:150637800-150639000	Enhancers	Stomach Smooth Muscle	stomach
44	chr7:150637800-150639800	Enhancers	Rectal Smooth Muscle	rectum
45	chr7:150637800-150640400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr7:150637800-150642400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr7:150637800-150652400	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links