Variant report

Variant	rs11657388
Chromosome Location	chr17:45820707-45820708
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45776258..45776778-chr17:45820261..45820767,2	MCF-7	breast:
2	chr17:45770256..45772710-chr17:45820237..45822227,2	MCF-7	breast:
3	chr17:45819448..45824573-chr17:45826000..45830135,4	K562	blood:
4	chr17:45811192..45813329-chr17:45818442..45821780,3	K562	blood:
5	chr17:45762090..45764390-chr17:45820597..45823079,2	K562	blood:

Variant related genes	Relation type
ENSG00000198933	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11079786	0.84[ASW][hapmap];0.85[LWK][hapmap];0.90[YRI][hapmap]
rs11079788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11650354	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11650451	0.89[CEU][hapmap]
rs11653146	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11657479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11658895	0.86[AMR][1000 genomes]
rs12451801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16947078	0.89[CEU][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes]
rs2074190	0.84[ASW][hapmap]
rs41321047	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41519545	0.96[ASN][1000 genomes]
rs56172120	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57171311	0.86[AMR][1000 genomes]
rs66490177	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831632	0.96[ASN][1000 genomes]
rs7502875	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908571	chr17:45765249-45821510	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	nsv2071	chr17:45801503-45844229	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11657388	C17orf57	cis	cerebellum	SCAN
rs11657388	C17orf57	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45811400-45822000	Weak transcription	Right Atrium	heart
2	chr17:45819200-45824000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:45819600-45823000	Genic enhancers	Primary T cells fromperipheralblood	blood
4	chr17:45819800-45820800	Enhancers	Dnd41	blood
5	chr17:45820400-45821600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr17:45820400-45821600	Weak transcription	K562	blood
7	chr17:45820400-45821800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr17:45820400-45822000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr17:45820400-45824000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr17:45820600-45820800	Enhancers	Spleen	Spleen
11	chr17:45820600-45820800	Bivalent Enhancer	HepG2	liver
12	chr17:45820600-45821600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr17:45820600-45821600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr17:45820600-45821800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr17:45820600-45821800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr17:45820600-45821800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr17:45820600-45822000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr17:45820600-45822000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr17:45820600-45822400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr17:45820600-45822800	Weak transcription	GM12878-XiMat	blood
21	chr17:45820600-45823600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr17:45820600-45823800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr17:45820600-45826200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr17:45820600-45830400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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