Variant report

Variant	rs17546202
Chromosome Location	chr7:50727564-50727565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50721573..50723142-chr7:50725744..50727999,2	K562	blood:
2	chr7:50726075..50728513-chr7:50729763..50731753,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs17152083	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs17449259	0.87[AMR][1000 genomes]
rs17544866	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17544971	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17545714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17546034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17546062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17546146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17546223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17547664	0.88[CHB][hapmap]
rs17547986	0.88[CHB][hapmap];0.88[CHD][hapmap]
rs17548938	0.85[CHB][hapmap]
rs2190496	0.89[CHB][hapmap]
rs3819431	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245558	0.88[CHB][hapmap]
rs4612291	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4947816	0.88[CHB][hapmap]
rs55716906	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55857758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56037477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60767324	1.00[ASN][1000 genomes]
rs6948959	0.89[CHB][hapmap]
rs73113031	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73113047	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73113061	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73113067	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73113068	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73113089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73113093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73113096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73113099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73114804	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73114807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73114809	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73114873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114877	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114878	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114889	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114899	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114901	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7456111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs956117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1032882	chr7:50611138-50775257	Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv538834	chr7:50611138-50775257	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17546202	VSTM2A	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50694200-50729200	Weak transcription	Hela-S3	cervix
2	chr7:50701000-50733600	Weak transcription	A549	lung
3	chr7:50701200-50728800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr7:50701200-50731200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:50701200-50733600	Weak transcription	K562	blood
6	chr7:50701400-50729000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr7:50706400-50744000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:50707200-50748600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:50707800-50727600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr7:50708200-50729400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr7:50710000-50733200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr7:50710000-50743600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:50710000-50758200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:50710200-50729400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:50715600-50740600	Weak transcription	Brain Germinal Matrix	brain
16	chr7:50716600-50727800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:50716600-50740200	Weak transcription	Fetal Intestine Large	intestine
18	chr7:50717200-50729400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:50718600-50728000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:50718600-50729200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:50719800-50729000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr7:50720600-50739400	Enhancers	Right Atrium	heart
23	chr7:50721400-50727800	Weak transcription	Primary T cells from cord blood	blood
24	chr7:50721400-50729200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr7:50721600-50727600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr7:50722000-50727800	Weak transcription	Gastric	stomach
27	chr7:50722000-50737600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:50722200-50727600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr7:50722200-50727600	Weak transcription	Fetal Thymus	thymus
30	chr7:50722200-50728800	Weak transcription	Fetal Brain Male	brain
31	chr7:50723000-50732400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:50723600-50728400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr7:50723600-50735200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr7:50723800-50727600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:50724000-50728200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr7:50724000-50728400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:50724000-50728400	Enhancers	Liver	Liver
38	chr7:50724200-50742800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:50724400-50727800	Weak transcription	Esophagus	oesophagus
40	chr7:50724800-50727600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr7:50725200-50727800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr7:50725200-50728000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr7:50725400-50727800	Weak transcription	GM12878-XiMat	blood
44	chr7:50725400-50737600	Enhancers	Psoas Muscle	Psoas
45	chr7:50725600-50727600	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr7:50725800-50728400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr7:50726000-50729800	Weak transcription	Brain Hippocampus Middle	brain
48	chr7:50726000-50729800	Weak transcription	Osteobl	bone
49	chr7:50726000-50731000	Weak transcription	Aorta	Aorta
50	chr7:50726000-50734200	Weak transcription	Fetal Heart	heart

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