Variant report

Variant	rs2758862
Chromosome Location	chr6:39239122-39239123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:39193484..39195491-chr6:39238843..39241224,2	K562	blood:
2	chr6:39238194..39240550-chr6:39241911..39243898,2	K562	blood:
3	chr6:39173237..39177206-chr6:39236026..39240576,5	MCF-7	breast:
4	chr6:39235849..39239507-chr6:39267408..39272188,7	MCF-7	breast:
5	chr6:39233505..39239976-chr6:39262109..39267318,6	MCF-7	breast:
6	chr6:39195043..39199102-chr6:39233396..39239186,7	MCF-7	breast:
7	chr6:39160661..39163154-chr6:39237331..39239168,2	MCF-7	breast:
8	chr6:39236564..39239398-chr6:39277207..39280181,2	MCF-7	breast:
9	chr6:39237190..39240116-chr6:39261691..39264000,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10807204	0.82[GIH][hapmap]
rs10807205	0.85[GIH][hapmap]
rs12194951	0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12197500	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12201021	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214300	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214342	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891847	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16891848	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2395721	0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap]
rs2758875	0.84[ASN][1000 genomes]
rs2815022	0.99[ASN][1000 genomes]
rs34625110	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6940480	0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs9349112	0.95[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs9349113	0.82[ASN][1000 genomes]
rs9367000	0.81[ASN][1000 genomes]
rs9367001	0.80[ASN][1000 genomes]
rs9367002	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9369111	0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs9380846	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs9394581	0.84[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9394582	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2758862	KCNK17	cis	multi-tissue	Pritchard

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39232000-39239800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr6:39233600-39240200	Enhancers	Placenta	Placenta
3	chr6:39236000-39241200	Weak transcription	Colonic Mucosa	Colon
4	chr6:39236000-39241400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:39236600-39241000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:39236800-39239800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:39236800-39240000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:39236800-39240000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:39237000-39239800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:39237000-39240000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr6:39237200-39239600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:39237200-39240200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:39237400-39239400	Enhancers	Placenta Amnion	Placenta Amnion
14	chr6:39237800-39240000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:39237800-39241200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:39238200-39241400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr6:39238400-39243200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:39238600-39243000	Weak transcription	Spleen	Spleen
19	chr6:39239000-39239400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:39239000-39241200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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