Variant report

Variant	rs1247359
Chromosome Location	chr6:161340682-161340683
allele	C/G
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	GATA3	chr6:161340609-161341138	SK-N-SH	brain:	n/a	n/a
2	FOS	chr6:161340680-161341221	MCF10A-Er-Src	breast:	n/a	chr6:161340727-161340735 chr6:161340884-161340896
3	GATA3	chr6:161340639-161341280	SK-N-SH	brain:	n/a	n/a
4	NFIC	chr6:161340636-161341296	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr6:161340568-161341282	SK-N-SH	brain:	n/a	n/a
6	JUND	chr6:161340605-161341299	SK-N-SH	brain:	n/a	chr6:161340727-161340735 chr6:161340884-161340896
7	JUND	chr6:161340665-161341089	SK-N-SH	brain:	n/a	chr6:161340727-161340735 chr6:161340884-161340896
8	FOSL2	chr6:161340658-161341110	SK-N-SH	brain:	n/a	chr6:161340727-161340735 chr6:161340884-161340896
9	TCF12	chr6:161340576-161341315	SK-N-SH	brain:	n/a	n/a
10	MAX	chr6:161340560-161341411	Hela-S3	cervix:	n/a	chr6:161341214-161341223
11	NFIC	chr6:161340666-161341194	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
ENSG00000224371	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1247293	1.00[ASN][1000 genomes]
rs1247295	1.00[ASN][1000 genomes]
rs1247297	1.00[ASN][1000 genomes]
rs1247301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1247303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1247311	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs1247348	0.89[ASN][1000 genomes]
rs1247349	0.89[ASN][1000 genomes]
rs1247351	0.89[ASN][1000 genomes]
rs1247352	0.89[ASN][1000 genomes]
rs1247354	0.91[ASN][1000 genomes]
rs1247355	0.90[ASN][1000 genomes]
rs1247356	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.92[ASN][1000 genomes]
rs1937467	0.86[ASN][1000 genomes]
rs1937475	0.93[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2248982	0.84[ASN][1000 genomes]
rs2465845	0.86[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs2489957	0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2489959	0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs935184	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9365233	0.89[ASW][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830853	chr6:161180005-161376481	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2422347	chr6:161211171-161442377	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1247359	QKI	cis	parietal	SCAN
rs1247359	SOD2	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161334200-161347800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:161338000-161341800	Enhancers	Fetal Intestine Small	intestine
3	chr6:161338600-161341600	Enhancers	Fetal Intestine Large	intestine
4	chr6:161338800-161341600	Enhancers	Stomach Mucosa	stomach
5	chr6:161339400-161340800	Enhancers	Pancreas	Pancrea
6	chr6:161339400-161341200	Enhancers	Duodenum Mucosa	Duodenum
7	chr6:161339400-161341600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:161339400-161341600	Enhancers	Hela-S3	cervix
9	chr6:161339400-161341600	Enhancers	HMEC	breast
10	chr6:161340000-161341400	Enhancers	HepG2	liver
11	chr6:161340000-161352000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:161340200-161341600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:161340200-161341600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr6:161340200-161341600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:161340200-161341600	Enhancers	Aorta	Aorta
16	chr6:161340400-161340800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:161340400-161340800	Enhancers	NHDF-Ad	bronchial
18	chr6:161340400-161341400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:161340400-161341400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:161340400-161341400	Enhancers	GM12878-XiMat	blood
21	chr6:161340400-161341600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:161340400-161341600	Enhancers	NHEK	skin
23	chr6:161340400-161341800	Enhancers	Osteobl	bone
24	chr6:161340400-161343400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:161340600-161340800	Flanking Active TSS	Liver	Liver
26	chr6:161340600-161341000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:161340600-161341400	Weak transcription	Placenta	Placenta
28	chr6:161340600-161341400	Enhancers	HSMMtube	muscle
29	chr6:161340600-161341400	Enhancers	NH-A	brain
30	chr6:161340600-161341600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:161340600-161341600	Enhancers	HSMM	muscle

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