Variant report

Variant	rs2814985
Chromosome Location	chr6:34548296-34548297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr6:34548123-34548459	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:34547296-34550215	K562	blood:	n/a	n/a
3	POLR2A	chr6:34547379-34549606	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:34548239-34548320	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:34536153..34538160-chr6:34545936..34548526,2	MCF-7	breast:
2	chr6:34546025..34550946-chr6:34551862..34556143,7	K562	blood:
3	chr6:34544544..34547164-chr6:34547916..34551672,4	K562	blood:

Variant related genes	Relation type
ENSG00000196114	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11752260	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092344	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252551	0.81[YRI][hapmap]
rs2492859	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492863	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744938	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2744939	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744942	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744947	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744954	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744955	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744956	0.90[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744963	0.81[YRI][hapmap]
rs2744964	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744965	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744966	0.81[YRI][hapmap]
rs2744971	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744972	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744977	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764205	0.90[CEU][hapmap]
rs2814943	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814944	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2814948	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2814950	0.81[YRI][hapmap]
rs2814973	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814977	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814983	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814986	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814990	0.81[YRI][hapmap]
rs2814993	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814994	0.90[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814996	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814998	0.81[YRI][hapmap]
rs2815003	0.81[YRI][hapmap]
rs2815005	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800457	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800461	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56930444	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6907508	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938239	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462007	0.90[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs9462014	1.00[CHD][hapmap];0.89[GIH][hapmap]
rs9469864	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer 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 miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv885788	chr6:34464010-34551912	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv1033583	chr6:34471572-34828372	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	38 gene(s)	inside rSNPs	diseases
8	nsv516578	chr6:34483015-34561585	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv885792	chr6:34507311-34607958	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv1015306	chr6:34509776-34549107	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
11	nsv1032763	chr6:34509776-34552797	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
12	nsv1025472	chr6:34509776-34555969	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
13	nsv1033534	chr6:34516588-34555969	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
14	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv823667	chr6:34533015-34592524	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
16	nsv818410	chr6:34538544-34579431	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
17	nsv830640	chr6:34542489-34714677	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2814985	C6orf107	Cis_1M	lymphoblastoid	RTeQTL
rs2814985	C6orf106	Cis_1M	lymphoblastoid	RTeQTL
rs2814985	C6orf106	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34528800-34551400	Weak transcription	Right Atrium	heart
2	chr6:34535600-34563200	Weak transcription	A549	lung
3	chr6:34536800-34554400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:34536800-34556600	Weak transcription	Hela-S3	cervix
5	chr6:34537400-34552800	Weak transcription	Fetal Intestine Large	intestine
6	chr6:34538000-34555400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:34538800-34550600	Weak transcription	Esophagus	oesophagus
8	chr6:34538800-34552600	Weak transcription	Right Ventricle	heart
9	chr6:34539600-34552800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:34540200-34548800	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:34540800-34554000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:34541400-34548600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:34541600-34553200	Weak transcription	Lung	lung
14	chr6:34541800-34553400	Weak transcription	HepG2	liver
15	chr6:34542000-34553000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:34542200-34548600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:34542200-34555400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:34542400-34553800	Weak transcription	Liver	Liver
19	chr6:34543200-34548600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr6:34543200-34548600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:34543200-34549000	Weak transcription	Fetal Intestine Small	intestine
22	chr6:34543200-34552200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:34544200-34548600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:34544200-34548600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:34544200-34548600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:34544200-34555000	Weak transcription	Pancreas	Pancrea
27	chr6:34544400-34548600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:34544400-34548600	Weak transcription	Fetal Lung	lung
29	chr6:34544400-34551200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:34544600-34548600	Weak transcription	Spleen	Spleen
31	chr6:34544600-34549000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr6:34544600-34553600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:34544600-34553800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:34544800-34549000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr6:34544800-34551000	Weak transcription	Placenta	Placenta
36	chr6:34545000-34550800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr6:34545000-34554400	Weak transcription	NHEK	skin
38	chr6:34545200-34548600	Weak transcription	Brain Anterior Caudate	brain
39	chr6:34545200-34552600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:34545200-34552800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:34545400-34549000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr6:34545400-34554000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr6:34545600-34550000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:34545800-34551400	Weak transcription	Primary T cells from cord blood	blood
45	chr6:34545800-34552600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:34545800-34553200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr6:34546000-34554000	Weak transcription	Fetal Thymus	thymus
48	chr6:34546000-34559800	Weak transcription	HSMM	muscle
49	chr6:34546200-34553000	Weak transcription	K562	blood
50	chr6:34546400-34555600	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links