Variant report

Variant	rs973205
Chromosome Location	chr6:54729949-54729950
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54704497..54716767-chr6:54728797..54750947,71	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction
ENSG00000224984	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10456176	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10948866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948867	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10948870	0.94[ASN][1000 genomes]
rs1155749	0.94[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs12192659	0.89[CEU][hapmap];0.94[CHB][hapmap];0.83[EUR][1000 genomes]
rs12208341	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12208348	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12211168	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1393776	0.88[CHB][hapmap]
rs1472679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs148109	0.81[CEU][hapmap]
rs171224	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs181155	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs1963697	0.88[CHB][hapmap]
rs2143798	0.83[ASN][1000 genomes]
rs2179786	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs2207025	0.85[CEU][hapmap]
rs2207026	0.87[CEU][hapmap]
rs239781	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs239783	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs239790	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs239796	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs239801	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs239837	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs2816811	0.81[CEU][hapmap]
rs2816812	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs4715489	0.94[ASN][1000 genomes]
rs6459034	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs6910384	0.94[ASN][1000 genomes]
rs6918402	0.93[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926997	0.88[CHB][hapmap]
rs6937970	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7741915	0.82[CHB][hapmap]
rs7752349	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7761336	0.94[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs7765721	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs924712	0.85[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs931766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs931767	0.95[ASN][1000 genomes]
rs9349740	0.88[CHB][hapmap]
rs9370332	0.82[CHD][hapmap]
rs9370345	0.87[CHB][hapmap]
rs9382403	0.88[CHB][hapmap]
rs9396003	0.94[ASN][1000 genomes]
rs971526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs988913	0.88[CHB][hapmap]

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	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr6:54715400-54731200	Weak transcription	Hela-S3	cervix
2	chr6:54721200-54730000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:54725400-54731400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:54725600-54737400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:54725600-54737600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:54725800-54730000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:54725800-54730000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:54725800-54730000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:54726600-54739600	Weak transcription	Small Intestine	intestine
10	chr6:54727000-54730000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:54727000-54730600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:54727200-54730000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:54727200-54731400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:54727200-54732800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:54727200-54748800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:54727400-54730000	Weak transcription	Fetal Kidney	kidney
17	chr6:54727400-54740400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:54727400-54743800	Weak transcription	Pancreas	Pancrea
19	chr6:54728600-54732800	Weak transcription	NHEK	skin
20	chr6:54729000-54731800	Enhancers	Fetal Heart	heart
21	chr6:54729200-54733400	Weak transcription	HMEC	breast
22	chr6:54729400-54730000	Weak transcription	Fetal Intestine Large	intestine
23	chr6:54729400-54731200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:54729800-54730200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr6:54729800-54730200	Enhancers	Gastric	stomach
26	chr6:54729800-54730200	Enhancers	Stomach Mucosa	stomach
27	chr6:54729800-54732200	Enhancers	Fetal Intestine Small	intestine

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