Variant report

Variant	rs11709517
Chromosome Location	chr3:43326887-43326888
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:43305979..43308043-chr3:43325669..43327950,2	MCF-7	breast:
2	chr3:43314193..43316141-chr3:43325214..43327876,2	K562	blood:
3	chr3:43325116..43327718-chr3:43329418..43331490,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1026887	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11130000	0.91[EUR][1000 genomes]
rs11706123	0.82[AMR][1000 genomes]
rs11708097	0.86[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11708173	1.00[ASW][hapmap];0.87[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap]
rs11709165	0.82[AMR][1000 genomes]
rs11710079	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs11710107	0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs11710253	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710486	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11710955	0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs11711651	0.89[AMR][1000 genomes]
rs11711758	0.86[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11712075	0.94[EUR][1000 genomes]
rs11712894	0.82[AMR][1000 genomes]
rs11715609	0.87[EUR][1000 genomes]
rs11717380	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11717449	0.82[AMR][1000 genomes]
rs11718482	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11719258	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13061553	0.82[AMR][1000 genomes]
rs13079636	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes]
rs13082581	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13084604	0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs13097209	0.80[AFR][1000 genomes]
rs13098202	0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1384434	0.86[CEU][hapmap];0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs1471644	0.90[CHB][hapmap]
rs1482648	0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1482650	0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs1506615	0.86[EUR][1000 genomes]
rs1506616	0.86[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs17407870	0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs17407912	0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs17643558	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2086653	0.91[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2372433	0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2888312	0.82[CEU][hapmap];0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs34898315	0.82[AMR][1000 genomes]
rs35015014	0.84[AMR][1000 genomes]
rs35323779	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs35690908	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4564953	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6441775	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs66498110	0.94[EUR][1000 genomes]
rs67032102	0.84[AMR][1000 genomes]
rs6767983	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6768557	0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs6775337	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs6781290	0.82[AMR][1000 genomes]
rs6782442	0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs73072960	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73075063	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752008	chr3:43285369-43360879	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1009102	chr3:43285369-43369712	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3420235	chr3:43326048-43330246	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv876732	chr3:43326887-43360879	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11709517	TMEM42	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43318800-43327800	Weak transcription	Small Intestine	intestine
2	chr3:43321600-43327000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:43324000-43327200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:43325200-43327400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:43326200-43327200	Weak transcription	NHEK	skin
6	chr3:43326200-43327400	Enhancers	Fetal Brain Male	brain
7	chr3:43326400-43327400	Enhancers	Adipose Nuclei	Adipose
8	chr3:43326400-43327600	Enhancers	HUVEC	blood vessel
9	chr3:43326600-43327000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr3:43326600-43327000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
11	chr3:43326600-43327000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
12	chr3:43326600-43327000	Bivalent Enhancer	HepG2	liver
13	chr3:43326600-43327200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr3:43326600-43327200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:43326600-43327200	Enhancers	Fetal Brain Female	brain
16	chr3:43326600-43327400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr3:43326600-43327400	Enhancers	Thymus	Thymus
18	chr3:43326800-43327400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
19	chr3:43326800-43327600	Enhancers	Fetal Thymus	thymus
20	chr3:43326800-43327600	Enhancers	Spleen	Spleen

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