Variant report

Variant	rs7604
Chromosome Location	chr6:38643796-38643797
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10484855	0.88[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1130534	0.83[EUR][1000 genomes]
rs11751782	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206711	1.00[ASN][1000 genomes]
rs12212784	1.00[ASN][1000 genomes]
rs13191302	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194237	0.89[EUR][1000 genomes]
rs13196530	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196708	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198900	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13199033	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13202862	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13203443	0.88[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207160	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13209846	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210334	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13212218	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13213257	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214969	0.90[EUR][1000 genomes]
rs13215896	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13217234	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13218305	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219252	0.88[CEU][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219395	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13219781	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1698998	1.00[ASN][1000 genomes]
rs17544311	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17544868	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1937782	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180106	1.00[CHD][hapmap]
rs2654449	1.00[ASN][1000 genomes]
rs28360530	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34349982	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34360712	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34408317	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34470929	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34519749	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34637217	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34695044	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34897279	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34962226	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34971977	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35147121	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35152718	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35207097	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35266471	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35364976	0.94[EUR][1000 genomes]
rs35388596	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35901431	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35975219	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67457665	1.00[ASN][1000 genomes]
rs6932648	1.00[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs71544423	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71571331	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71571332	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71571336	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72856580	1.00[ASN][1000 genomes]
rs73416349	1.00[ASN][1000 genomes]
rs73416350	1.00[ASN][1000 genomes]
rs73416351	1.00[ASN][1000 genomes]
rs7451595	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7746400	1.00[ASN][1000 genomes]
rs7750789	1.00[ASN][1000 genomes]
rs7762397	1.00[ASN][1000 genomes]
rs9369075	0.81[EUR][1000 genomes]
rs9380782	1.00[LWK][hapmap]
rs9394523	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9394524	1.00[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs9462450	0.81[EUR][1000 genomes]
rs963720	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.94[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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2758049	chr6:38588969-38711085	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2759421	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv427754	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv428144	chr6:38588969-38711085	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7604	MAPK13	cis	parietal	SCAN
rs7604	TFEB	cis	cerebellum	SCAN
rs7604	KCNK5	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38609000-38645200	Weak transcription	Fetal Intestine Small	intestine
2	chr6:38609000-38645600	Weak transcription	Left Ventricle	heart
3	chr6:38612800-38648400	Weak transcription	Brain Anterior Caudate	brain
4	chr6:38612800-38652800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:38614800-38654800	Weak transcription	Brain Angular Gyrus	brain
6	chr6:38615200-38645200	Weak transcription	Ovary	ovary
7	chr6:38615200-38649400	Weak transcription	Fetal Brain Male	brain
8	chr6:38618200-38646200	Weak transcription	Aorta	Aorta
9	chr6:38618800-38643800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:38620200-38646200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:38622400-38643800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:38623400-38645600	Weak transcription	Brain Substantia Nigra	brain
13	chr6:38624200-38646200	Weak transcription	Lung	lung
14	chr6:38626400-38645200	Weak transcription	Fetal Stomach	stomach
15	chr6:38629400-38644800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:38640000-38649400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:38640000-38649400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr6:38640000-38652400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr6:38640200-38650200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:38641000-38646200	Weak transcription	Brain Germinal Matrix	brain
21	chr6:38641000-38646200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr6:38641000-38654800	Weak transcription	Fetal Heart	heart
23	chr6:38641200-38644400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:38641200-38646200	Weak transcription	Esophagus	oesophagus
25	chr6:38641200-38670000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:38641400-38649400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:38641600-38646200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:38641600-38646200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr6:38641600-38646200	Weak transcription	Spleen	Spleen
30	chr6:38641600-38668000	Weak transcription	NHLF	lung
31	chr6:38641800-38645600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:38641800-38645800	Weak transcription	Colonic Mucosa	Colon
33	chr6:38641800-38649400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr6:38641800-38650600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:38641800-38651000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr6:38641800-38654800	Weak transcription	Pancreas	Pancrea
37	chr6:38642000-38644400	Strong transcription	Primary T cells from cord blood	blood
38	chr6:38642000-38648400	Weak transcription	Small Intestine	intestine
39	chr6:38642000-38650800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr6:38642000-38652600	Weak transcription	Stomach Mucosa	stomach
41	chr6:38642000-38657600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr6:38642200-38645000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr6:38642200-38651400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:38642200-38652200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:38642200-38656400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:38642400-38644000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr6:38642400-38645600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:38642400-38645800	Strong transcription	Osteobl	bone
49	chr6:38642400-38647200	Strong transcription	Adipose Nuclei	Adipose
50	chr6:38642400-38647200	Strong transcription	Fetal Intestine Large	intestine

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