Variant report

Variant	rs2815020
Chromosome Location	chr6:39238278-39238279
allele	A/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:39238194..39240550-chr6:39241911..39243898,2	K562	blood:
2	chr6:39228773..39231561-chr6:39235112..39238664,3	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	chr6:39236174..39238959-chr6:39247299..39249650,2	MCF-7	breast:
6	chr6:39233505..39239976-chr6:39262109..39267318,6	MCF-7	breast:
7	chr6:39195043..39199102-chr6:39233396..39239186,7	MCF-7	breast:
8	chr6:39160661..39163154-chr6:39237331..39239168,2	MCF-7	breast:
9	chr6:39236564..39239398-chr6:39277207..39280181,2	MCF-7	breast:
10	chr6:39237190..39240116-chr6:39261691..39264000,2	K562	blood:
11	chr6:39235093..39238743-chr6:39267391..39271695,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1005995	0.83[ASN][1000 genomes]
rs1182864	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs12191604	0.99[ASN][1000 genomes]
rs12191756	0.98[ASN][1000 genomes]
rs12198547	0.87[ASN][1000 genomes]
rs12198665	0.85[ASN][1000 genomes]
rs2253582	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2395719	0.91[ASN][1000 genomes]
rs2395720	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2758863	0.85[ASN][1000 genomes]
rs2758864	0.99[ASN][1000 genomes]
rs2758865	0.97[ASN][1000 genomes]
rs2758866	0.99[ASN][1000 genomes]
rs2758867	0.99[ASN][1000 genomes]
rs2758868	0.97[ASN][1000 genomes]
rs2758869	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2758871	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2758872	0.94[ASN][1000 genomes]
rs2758874	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2758912	0.81[GIH][hapmap]
rs2815019	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2815024	0.99[ASN][1000 genomes]
rs2815025	0.98[ASN][1000 genomes]
rs2815026	0.99[ASN][1000 genomes]
rs2815027	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2815028	0.99[ASN][1000 genomes]
rs2815029	0.99[ASN][1000 genomes]
rs2815030	0.93[ASN][1000 genomes]
rs2815031	0.99[ASN][1000 genomes]
rs2815032	0.98[ASN][1000 genomes]
rs2815035	0.98[ASN][1000 genomes]
rs2815036	0.98[ASN][1000 genomes]
rs2815037	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2815038	0.98[ASN][1000 genomes]
rs2815039	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2815040	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2815041	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2815042	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2815044	0.94[ASN][1000 genomes]
rs2815045	0.90[ASN][1000 genomes]
rs2815061	0.82[ASN][1000 genomes]
rs34170020	0.95[ASN][1000 genomes]
rs34343201	0.95[ASN][1000 genomes]
rs4714233	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7746595	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394580	0.91[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2815020	KCNK17	cis	multi-tissue	Pritchard
rs2815020	LOC221442	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39224400-39238400	Weak transcription	Spleen	Spleen
2	chr6:39232000-39239800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr6:39233600-39240200	Enhancers	Placenta	Placenta
4	chr6:39234800-39239000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:39236000-39241200	Weak transcription	Colonic Mucosa	Colon
6	chr6:39236000-39241400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:39236600-39238800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:39236600-39241000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:39236800-39239800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:39236800-39240000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:39236800-39240000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:39237000-39239800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:39237000-39240000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:39237200-39239600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:39237200-39240200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:39237400-39238400	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr6:39237400-39239400	Enhancers	Placenta Amnion	Placenta Amnion
18	chr6:39237600-39238400	Enhancers	Fetal Intestine Small	intestine
19	chr6:39237800-39240000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:39237800-39241200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:39238200-39241400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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