Variant report

Variant	rs3800018
Chromosome Location	chr6:57069606-57069607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:57062290..57064977-chr6:57069550..57072022,3	MCF-7	breast:
2	chr6:57067110..57071080-chr6:57071406..57075430,5	K562	blood:
3	chr6:57048931..57051887-chr6:57068074..57070259,2	K562	blood:
4	chr6:57065751..57068051-chr6:57069348..57071152,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1020550	0.80[ASN][1000 genomes]
rs10484410	1.00[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs11398	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12190575	0.90[ASN][1000 genomes]
rs12192222	0.90[ASN][1000 genomes]
rs12194288	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12194407	0.90[ASN][1000 genomes]
rs12198801	0.90[ASN][1000 genomes]
rs12201039	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210597	0.81[CEU][hapmap]
rs12211901	1.00[ASN][1000 genomes]
rs12214882	1.00[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs1411578	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1547226	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs16888392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17619360	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs3800019	0.80[CEU][hapmap];0.83[TSI][hapmap]
rs3800023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3800025	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3996934	0.80[ASN][1000 genomes]
rs3996935	0.80[ASN][1000 genomes]
rs3996936	0.80[ASN][1000 genomes]
rs4523090	0.80[ASN][1000 genomes]
rs4631287	0.80[ASN][1000 genomes]
rs6459178	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs6936506	0.90[ASN][1000 genomes]
rs72868608	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7744316	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs7748120	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7748453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7753547	0.80[ASN][1000 genomes]
rs7756421	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs7764446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7771115	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs9396256	0.80[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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv462949	chr6:56973902-57098973	ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv603190	chr6:56973902-57098973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3800018	BEND6	cis	cerebellum	SCAN
rs3800018	RAB23	cis	lymphoblastoid	seeQTL
rs3800018	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs3800018	BEND6	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:57038000-57081600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:57038400-57072800	Weak transcription	Pancreas	Pancrea
3	chr6:57038400-57079600	Weak transcription	Fetal Brain Female	brain
4	chr6:57039000-57086000	Weak transcription	Thymus	Thymus
5	chr6:57048200-57072200	Weak transcription	Fetal Brain Male	brain
6	chr6:57049000-57072600	Weak transcription	Psoas Muscle	Psoas
7	chr6:57049400-57085000	Weak transcription	Aorta	Aorta
8	chr6:57050800-57072600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr6:57056600-57086000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:57057200-57081200	Weak transcription	HMEC	breast
11	chr6:57057600-57081200	Weak transcription	Fetal Intestine Small	intestine
12	chr6:57057800-57071400	Weak transcription	Fetal Thymus	thymus
13	chr6:57058000-57074200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr6:57058000-57080800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:57058200-57072800	Weak transcription	K562	blood
16	chr6:57058200-57079200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:57058200-57085800	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:57058400-57071400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:57058400-57072800	Weak transcription	GM12878-XiMat	blood
20	chr6:57058400-57078800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:57058800-57070200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:57058800-57071200	Weak transcription	HUVEC	blood vessel
23	chr6:57058800-57081000	Weak transcription	NHEK	skin
24	chr6:57058800-57084000	Weak transcription	Dnd41	blood
25	chr6:57059200-57084000	Weak transcription	Hela-S3	cervix
26	chr6:57060600-57080600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:57061400-57070800	Weak transcription	Ovary	ovary
28	chr6:57061600-57079600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:57062600-57084800	Weak transcription	HSMM	muscle
30	chr6:57064000-57071200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:57064200-57070200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:57064200-57077800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:57064400-57070600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:57064400-57070800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:57064400-57071200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr6:57064400-57077400	Weak transcription	Fetal Stomach	stomach
37	chr6:57064400-57077400	Weak transcription	HepG2	liver
38	chr6:57064400-57079000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:57064400-57079400	Weak transcription	NHLF	lung
40	chr6:57064400-57084000	Weak transcription	NH-A	brain
41	chr6:57064400-57085000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:57064400-57086200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:57065000-57070600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr6:57065000-57085000	Weak transcription	A549	lung
45	chr6:57065800-57070200	Weak transcription	HSMMtube	muscle
46	chr6:57065800-57070200	Weak transcription	Osteobl	bone
47	chr6:57065800-57070800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:57067400-57070000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:57067400-57070800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:57067400-57071200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links