Variant report

Variant	rs11657479
Chromosome Location	chr17:45822901-45822902
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45811931..45814457-chr17:45821701..45824432,2	MCF-7	breast:
2	chr17:45813787..45815804-chr17:45822257..45825163,2	MCF-7	breast:
3	chr17:45819448..45824573-chr17:45826000..45830135,4	K562	blood:
4	chr17:45794462..45797278-chr17:45822164..45823820,2	MCF-7	breast:
5	chr17:45762090..45764390-chr17:45820597..45823079,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11079788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11650354	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11650451	0.89[CEU][hapmap]
rs11651000	0.92[AFR][1000 genomes]
rs11652603	0.84[AFR][1000 genomes]
rs11653146	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11655306	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11657388	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	0.82[AMR][1000 genomes]
rs12451801	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16947078	0.89[CEU][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs17250932	0.96[AFR][1000 genomes]
rs41321047	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs41519545	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs57171311	0.82[AMR][1000 genomes]
rs66490177	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs72831632	0.98[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7502875	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][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	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	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
rs11657479	C17orf57	cis	parietal	SCAN
rs11657479	C17orf57	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45819200-45824000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr17:45819600-45823000	Genic enhancers	Primary T cells fromperipheralblood	blood
3	chr17:45820400-45824000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr17:45820600-45823600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr17:45820600-45823800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr17:45820600-45826200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr17:45820600-45830400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr17:45821200-45823800	Enhancers	Dnd41	blood
9	chr17:45821600-45823800	Enhancers	K562	blood
10	chr17:45821600-45824400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr17:45821800-45823400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr17:45821800-45823600	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr17:45821800-45823600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr17:45822000-45823000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr17:45822000-45823400	Enhancers	Primary hematopoietic stem cells	blood
16	chr17:45822000-45823600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr17:45822400-45823200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr17:45822400-45823200	Enhancers	Fetal Heart	heart
19	chr17:45822600-45823000	Bivalent Enhancer	Fetal Intestine Small	intestine
20	chr17:45822800-45823400	Strong transcription	GM12878-XiMat	blood
21	chr17:45822800-45823800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr17:45822800-45825200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr17:45822800-45825200	Weak transcription	Spleen	Spleen

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