Variant report

Variant	rs978565
Chromosome Location	chr6:11810083-11810084
allele	A/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	SMC3	chr6:11810069-11810923	Hela-S3	cervix:	n/a	n/a
2	MYC	chr6:11809986-11810722	MCF10A-Er-Src	breast:	n/a	chr6:11810588-11810597
3	TCF12	chr6:11809998-11810874	A549	lung:	n/a	chr6:11810472-11810480
4	TBP	chr6:11810049-11810766	Hela-S3	cervix:	n/a	n/a
5	NFIC	chr6:11810062-11810837	SK-N-SH	brain:	n/a	chr6:11810373-11810390 chr6:11810374-11810390
6	PRDM1	chr6:11810068-11810870	Hela-S3	cervix:	n/a	n/a
7	SP1	chr6:11810076-11810822	A549	lung:	n/a	n/a
8	NFIC	chr6:11810066-11810919	ECC-1	luminal epithelium:	n/a	chr6:11810373-11810390 chr6:11810374-11810390
9	ZNF263	chr6:11810044-11810654	HEK293-T-REx	kidney:	n/a	chr6:11810336-11810345
10	EP300	chr6:11810082-11810837	Hela-S3	cervix:	n/a	chr6:11810192-11810206
11	BRCA1	chr6:11810043-11810648	Hela-S3	cervix:	n/a	n/a
12	STAT3	chr6:11810037-11810742	Hela-S3	cervix:	n/a	chr6:11810189-11810200
13	NFIC	chr6:11810009-11810910	ECC-1	luminal epithelium:	n/a	chr6:11810373-11810390 chr6:11810374-11810390
14	POLR2A	chr6:11810045-11810750	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ADTRP	TF binding region
ENSG00000234427	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1014972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947579	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1569731	0.88[ASN][1000 genomes]
rs1569735	0.88[ASN][1000 genomes]
rs16871833	0.89[CEU][hapmap]
rs1883324	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1883325	0.89[CEU][hapmap]
rs1883326	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2143715	0.94[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs2179742	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3950186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4308554	0.84[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4310046	0.87[ASN][1000 genomes]
rs4404760	0.94[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4557506	0.87[ASN][1000 genomes]
rs4634440	0.88[ASN][1000 genomes]
rs6899747	0.89[ASN][1000 genomes]
rs6902916	0.82[CHB][hapmap]
rs6910363	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6936286	0.95[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6941812	0.89[CEU][hapmap]
rs6942235	0.89[CEU][hapmap]
rs7739256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7743245	0.94[CEU][hapmap]
rs7766152	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470184	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9470216	0.85[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][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	esv2758036	chr6:11679753-11822351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759407	chr6:11679753-11822351	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11796400-11810400	Weak transcription	Placenta	Placenta
2	chr6:11805000-11810400	Weak transcription	Right Atrium	heart
3	chr6:11805200-11810200	Weak transcription	NH-A	brain
4	chr6:11805400-11810200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:11806400-11810600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:11806600-11810200	Weak transcription	K562	blood
7	chr6:11807000-11810200	Weak transcription	Fetal Intestine Large	intestine
8	chr6:11807000-11810200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:11807200-11811000	Weak transcription	Lung	lung
10	chr6:11807400-11810200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr6:11807400-11810400	Weak transcription	Spleen	Spleen
12	chr6:11807600-11810400	Weak transcription	Esophagus	oesophagus
13	chr6:11807600-11810400	Weak transcription	GM12878-XiMat	blood
14	chr6:11807600-11816400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:11808000-11814400	Weak transcription	Fetal Thymus	thymus
16	chr6:11809200-11810200	Enhancers	Hela-S3	cervix
17	chr6:11809200-11811400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr6:11809400-11810400	Weak transcription	Fetal Brain Male	brain
19	chr6:11809400-11810800	Enhancers	NHEK	skin
20	chr6:11809400-11811200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:11809400-11811200	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr6:11809400-11811200	Enhancers	HMEC	breast
23	chr6:11809600-11811400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr6:11809600-11811400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr6:11809800-11810400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:11809800-11810400	Enhancers	HSMM	muscle
27	chr6:11809800-11810400	Enhancers	Osteobl	bone
28	chr6:11809800-11810600	Enhancers	Brain Substantia Nigra	brain
29	chr6:11809800-11810600	Enhancers	Colonic Mucosa	Colon
30	chr6:11809800-11810600	Enhancers	Fetal Intestine Small	intestine
31	chr6:11809800-11810600	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr6:11809800-11810800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:11809800-11810800	Enhancers	HSMMtube	muscle
34	chr6:11809800-11811000	Enhancers	Brain Anterior Caudate	brain
35	chr6:11809800-11811000	Enhancers	Colon Smooth Muscle	Colon
36	chr6:11809800-11811000	Enhancers	Duodenum Mucosa	Duodenum
37	chr6:11809800-11811000	Flanking Active TSS	A549	lung
38	chr6:11809800-11811000	Enhancers	NHLF	lung
39	chr6:11809800-11811200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:11809800-11811200	Enhancers	Right Ventricle	heart
41	chr6:11809800-11811200	Enhancers	NHDF-Ad	bronchial
42	chr6:11809800-11811400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:11809800-11811400	Enhancers	Adipose Nuclei	Adipose
44	chr6:11809800-11811400	Enhancers	Ovary	ovary
45	chr6:11809800-11811400	Enhancers	Stomach Smooth Muscle	stomach
46	chr6:11809800-11811600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:11809800-11811800	Enhancers	Fetal Muscle Leg	muscle
48	chr6:11809800-11812000	Enhancers	Fetal Lung	lung
49	chr6:11809800-11812000	Enhancers	Stomach Mucosa	stomach
50	chr6:11809800-11812200	Enhancers	Cortex derived primary cultured neurospheres	brain

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