Variant report

Variant	rs1247361
Chromosome Location	chr6:161341269-161341270
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	chr6:161340639-161341280	SK-N-SH	brain:	n/a	n/a
2	EP300	chr6:161340813-161341269	Hela-S3	cervix:	n/a	n/a
3	NFIC	chr6:161340636-161341296	ECC-1	luminal epithelium:	n/a	n/a
4	TCF12	chr6:161340568-161341282	SK-N-SH	brain:	n/a	n/a
5	JUND	chr6:161340605-161341299	SK-N-SH	brain:	n/a	chr6:161340727-161340735 chr6:161340884-161340896
6	NFIC	chr6:161340724-161341301	SK-N-SH	brain:	n/a	n/a
7	CEBPB	chr6:161340765-161341328	IMR90	lung:	n/a	chr6:161340940-161340951
8	CEBPB	chr6:161340738-161341710	Hela-S3	cervix:	n/a	chr6:161340940-161340951 chr6:161341591-161341608
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	ELF1	chr6:161340693-161341297	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000224371	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11970528	0.82[ASN][1000 genomes]
rs1247294	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1247298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1247299	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1247300	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1247302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1247305	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247307	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1247308	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs1247309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1247310	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247312	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1247313	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247316	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247317	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247318	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247319	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247320	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247321	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247325	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1247326	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1247327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1247328	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1247329	1.00[CEU][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1247330	1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1247360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1247362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1247363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1247364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1247365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663025	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1937474	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2465834	0.81[JPT][hapmap]
rs2465869	0.80[ASN][1000 genomes]
rs2465870	0.82[ASN][1000 genomes]
rs2465871	0.80[ASN][1000 genomes]
rs2465876	0.93[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs2465877	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2465878	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2489955	0.86[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs2489956	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs581947	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs585649	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs591676	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62436898	0.94[ASN][1000 genomes]
rs638141	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs687701	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs935182	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs935183	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9355851	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9364580	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.80[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

No data

Chromatin state (count:27 , 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	chr6:161339400-161341600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:161339400-161341600	Enhancers	Hela-S3	cervix
7	chr6:161339400-161341600	Enhancers	HMEC	breast
8	chr6:161340000-161341400	Enhancers	HepG2	liver
9	chr6:161340000-161352000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:161340200-161341600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:161340200-161341600	Enhancers	Muscle Satellite Cultured Cells	--
12	chr6:161340200-161341600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:161340200-161341600	Enhancers	Aorta	Aorta
14	chr6:161340400-161341400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:161340400-161341400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:161340400-161341400	Enhancers	GM12878-XiMat	blood
17	chr6:161340400-161341600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:161340400-161341600	Enhancers	NHEK	skin
19	chr6:161340400-161341800	Enhancers	Osteobl	bone
20	chr6:161340400-161343400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:161340600-161341400	Weak transcription	Placenta	Placenta
22	chr6:161340600-161341400	Enhancers	HSMMtube	muscle
23	chr6:161340600-161341400	Enhancers	NH-A	brain
24	chr6:161340600-161341600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:161340600-161341600	Enhancers	HSMM	muscle
26	chr6:161340800-161341400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:161340800-161341800	Enhancers	Liver	Liver

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