Variant report

Variant	rs17682340
Chromosome Location	chr6:54721939-54721940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54718981..54722041-chr6:54724023..54729682,8	MCF-7	breast:
2	chr6:54718921..54722891-chr6:54723074..54726787,4	MCF-7	breast:
3	chr6:54721521..54725055-chr6:54731692..54735464,4	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12175211	1.00[JPT][hapmap]
rs12664791	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1507108	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs16885880	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs16886094	0.87[ASN][1000 genomes]
rs17682328	1.00[CEU][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17749547	0.92[EUR][1000 genomes]
rs2174144	1.00[CEU][hapmap]
rs62412606	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62412628	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62412629	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62412630	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62412631	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62412632	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62412635	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62412645	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62412646	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62412648	0.96[EUR][1000 genomes]
rs62412649	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62412651	0.87[ASN][1000 genomes]
rs62412652	0.87[ASN][1000 genomes]
rs62412655	0.87[ASN][1000 genomes]
rs62412657	0.87[ASN][1000 genomes]
rs62412658	0.87[ASN][1000 genomes]
rs62412659	0.87[ASN][1000 genomes]
rs62414960	0.83[ASN][1000 genomes]
rs62414962	0.83[ASN][1000 genomes]
rs7757553	1.00[CEU][hapmap]
rs9357819	0.92[EUR][1000 genomes]
rs9357821	1.00[CHB][hapmap]
rs9370340	0.85[TSI][hapmap]
rs9396000	0.92[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	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:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54712600-54725000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:54713200-54725600	Weak transcription	Gastric	stomach
3	chr6:54713400-54726400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:54715400-54731200	Weak transcription	Hela-S3	cervix
5	chr6:54720400-54722200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:54720400-54723000	Enhancers	Fetal Intestine Large	intestine
7	chr6:54720400-54723200	Enhancers	Fetal Intestine Small	intestine
8	chr6:54720800-54722400	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr6:54720800-54722400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr6:54720800-54722600	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr6:54721200-54722800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:54721200-54724000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:54721200-54724400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:54721200-54724400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:54721200-54724600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:54721200-54727000	Weak transcription	Fetal Kidney	kidney
17	chr6:54721200-54727000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr6:54721200-54730000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:54721400-54722600	Weak transcription	Stomach Mucosa	stomach
20	chr6:54721400-54723200	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr6:54721400-54724200	Weak transcription	HMEC	breast
22	chr6:54721400-54724400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:54721400-54724800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:54721400-54725000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:54721400-54725200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr6:54721400-54726200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr6:54721600-54723200	Strong transcription	NHEK	skin
28	chr6:54721600-54726400	Weak transcription	Placenta Amnion	Placenta Amnion

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