Variant report

Variant	rs1978208
Chromosome Location	chr7:50785448-50785449
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:50785108..50787997-chr7:50788315..50791487,3	K562	blood:
2	chr7:50777238..50779478-chr7:50783784..50785485,2	K562	blood:
3	chr7:50781516..50783338-chr7:50785082..50786881,2	K562	blood:
4	chr7:50782071..50785777-chr7:50859330..50862743,3	K562	blood:

Variant related genes	Relation type
ENSG00000106070	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10273302	0.86[CEU][hapmap]
rs10278363	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs11238339	0.87[CEU][hapmap]
rs12665949	0.86[CEU][hapmap]
rs13236710	0.81[CHB][hapmap]
rs17134002	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs17152120	0.81[CHB][hapmap]
rs1962390	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs1962391	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2329424	0.82[CEU][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2329490	0.82[ASN][1000 genomes]
rs2329491	0.81[ASN][1000 genomes]
rs2329494	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2529399	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2715119	1.00[CEU][hapmap];0.94[JPT][hapmap];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28599932	0.86[AFR][1000 genomes]
rs3779072	1.00[CEU][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4947828	0.82[ASN][1000 genomes]
rs4947861	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs6593182	0.87[CEU][hapmap]
rs6968827	0.82[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs7383871	0.82[ASN][1000 genomes]
rs7780348	0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7782797	0.82[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7794299	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1031138	chr7:50651793-50814881	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1978208	LOC100129427	cis	parietal	SCAN
rs1978208	VWC2	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50742600-50792000	Weak transcription	Primary T cells from cord blood	blood
2	chr7:50763400-50806800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:50766400-50785800	Weak transcription	Small Intestine	intestine
4	chr7:50772000-50791600	Weak transcription	K562	blood
5	chr7:50773000-50789200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:50773000-50807400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:50773600-50788600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr7:50773800-50786600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr7:50774800-50789200	Weak transcription	NHLF	lung
10	chr7:50776400-50786000	Weak transcription	HUVEC	blood vessel
11	chr7:50777600-50792600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr7:50778400-50789000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:50778600-50785600	Weak transcription	Fetal Intestine Small	intestine
14	chr7:50778800-50786800	Enhancers	Right Atrium	heart
15	chr7:50779400-50786000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr7:50780400-50786200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:50780400-50788400	Enhancers	Pancreas	Pancrea
18	chr7:50780600-50786400	Weak transcription	Osteobl	bone
19	chr7:50780600-50786600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:50780600-50795000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:50780600-50807600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr7:50780800-50801400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr7:50781000-50786000	Weak transcription	Brain Angular Gyrus	brain
24	chr7:50781000-50786400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:50781000-50787200	Enhancers	Lung	lung
26	chr7:50781000-50794800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:50781200-50786000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr7:50781200-50789200	Weak transcription	Colonic Mucosa	Colon
29	chr7:50781200-50791200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:50781200-50795600	Weak transcription	NHDF-Ad	bronchial
31	chr7:50781200-50797600	Weak transcription	HSMMtube	muscle
32	chr7:50781200-50798200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:50781400-50785800	Weak transcription	Fetal Lung	lung
34	chr7:50781400-50786400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr7:50781400-50789400	Weak transcription	Ovary	ovary
36	chr7:50781600-50785600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr7:50781600-50786800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:50781800-50785600	Weak transcription	Right Ventricle	heart
39	chr7:50781800-50786200	Weak transcription	Fetal Heart	heart
40	chr7:50781800-50786800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:50781800-50787600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr7:50781800-50789000	Weak transcription	Esophagus	oesophagus
43	chr7:50781800-50789400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:50782200-50788200	Enhancers	Stomach Mucosa	stomach
45	chr7:50782800-50787000	Enhancers	Psoas Muscle	Psoas
46	chr7:50782800-50788400	Enhancers	Gastric	stomach
47	chr7:50783000-50786800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:50783000-50789400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr7:50783000-50792000	Weak transcription	HSMM	muscle
50	chr7:50783200-50785800	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links