Variant report

Variant	rs7807841
Chromosome Location	chr7:6252458-6252459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10046499	1.00[JPT][hapmap]
rs10224504	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs10225119	1.00[JPT][hapmap]
rs10229323	0.83[ASN][1000 genomes]
rs10240510	1.00[JPT][hapmap]
rs10241174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10241580	0.89[ASN][1000 genomes]
rs10244640	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10245186	1.00[JPT][hapmap]
rs10247585	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs10252947	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10253501	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10255662	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10255914	1.00[JPT][hapmap]
rs10261217	1.00[JPT][hapmap]
rs10267982	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs10268916	1.00[CHB][hapmap]
rs10274992	0.94[ASN][1000 genomes]
rs10275021	1.00[JPT][hapmap]
rs10279137	1.00[JPT][hapmap]
rs10280585	1.00[JPT][hapmap]
rs11768047	1.00[JPT][hapmap]
rs11768749	1.00[JPT][hapmap]
rs11973228	0.81[EUR][1000 genomes]
rs11973659	0.81[EUR][1000 genomes]
rs11974681	0.81[EUR][1000 genomes]
rs12667392	1.00[JPT][hapmap]
rs13437890	1.00[JPT][hapmap]
rs17136048	1.00[JPT][hapmap]
rs35719886	0.86[AMR][1000 genomes]
rs41282682	0.81[EUR][1000 genomes]
rs55681139	0.81[EUR][1000 genomes]
rs56295477	0.81[EUR][1000 genomes]
rs59116230	0.82[AMR][1000 genomes]
rs59180903	0.84[ASN][1000 genomes]
rs6463540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs6463541	1.00[JPT][hapmap]
rs6463544	1.00[JPT][hapmap]
rs6942707	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6944071	1.00[JPT][hapmap]
rs6944216	0.84[ASN][1000 genomes]
rs6946205	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6949823	1.00[JPT][hapmap]
rs6953328	0.81[EUR][1000 genomes]
rs6955065	1.00[JPT][hapmap]
rs6957628	0.81[EUR][1000 genomes]
rs6958932	0.94[AMR][1000 genomes]
rs6960965	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6962767	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6969814	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6969863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6974814	1.00[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs73675887	0.81[EUR][1000 genomes]
rs7777433	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs7780269	1.00[JPT][hapmap]
rs7783018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7784025	0.89[ASN][1000 genomes]
rs7791225	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7800777	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7806404	1.00[CEU][hapmap]
rs7811590	0.81[EUR][1000 genomes]
rs7811721	0.81[EUR][1000 genomes]
rs886675	0.84[YRI][hapmap]
rs958329	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
2	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
3	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription 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 target site	138 gene(s)	inside rSNPs	diseases
4	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
5	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
6	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription 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 target site	127 gene(s)	inside rSNPs	diseases
7	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
8	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv530989	chr7:6176729-6438197	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv5629	chr7:6217866-6263131	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv482829	chr7:6231809-6407606	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv1032987	chr7:6246313-6373054	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer 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	8 gene(s)	inside rSNPs	diseases
14	nsv538714	chr7:6246313-6373054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7807841	CYTH3	cis	lymphoblastoid	seeQTL
rs7807841	PSCD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6228600-6257400	Weak transcription	Primary B cells from cord blood	blood
2	chr7:6229000-6259800	Weak transcription	NHEK	skin
3	chr7:6229400-6270600	Weak transcription	Gastric	stomach
4	chr7:6229800-6257600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:6238600-6261000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:6240800-6265400	Weak transcription	HSMM	muscle
7	chr7:6241000-6265200	Weak transcription	Fetal Stomach	stomach
8	chr7:6241200-6265600	Weak transcription	Fetal Intestine Small	intestine
9	chr7:6244400-6261400	Weak transcription	Fetal Muscle Leg	muscle
10	chr7:6246200-6259000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:6246400-6259000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr7:6246400-6259000	Weak transcription	A549	lung
13	chr7:6246600-6261200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr7:6249200-6257800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr7:6249600-6257600	Weak transcription	Right Atrium	heart
16	chr7:6249600-6259000	Weak transcription	Small Intestine	intestine
17	chr7:6249600-6265800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr7:6249800-6254800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:6249800-6257600	Weak transcription	Aorta	Aorta
20	chr7:6249800-6259000	Weak transcription	NHDF-Ad	bronchial
21	chr7:6249800-6261000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:6249800-6265400	Weak transcription	HSMMtube	muscle
23	chr7:6249800-6265600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:6251000-6253400	Weak transcription	Lung	lung
25	chr7:6251000-6257600	Weak transcription	Left Ventricle	heart
26	chr7:6251000-6257800	Weak transcription	Right Ventricle	heart
27	chr7:6252000-6252600	Weak transcription	K562	blood
28	chr7:6252000-6256200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr7:6252200-6252800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:6252400-6252600	Enhancers	Psoas Muscle	Psoas

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