Variant report

Variant	rs12790863
Chromosome Location	chr11:72979231-72979232
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:72978414..72980152-chr11:72985099..72986982,2	MCF-7	breast:
2	chr11:72974009..72977358-chr11:72978806..72983362,4	MCF-7	breast:
3	chr11:72978520..72980025-chr11:72999904..73002174,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171631	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10898913	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10898914	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10898915	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11235699	1.00[JPT][hapmap]
rs11235701	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11235703	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235705	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235707	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235708	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235709	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235710	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11235711	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11235712	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs11235713	1.00[ASN][1000 genomes]
rs12276627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12363628	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12787775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12790447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12794405	1.00[ASN][1000 genomes]
rs12801084	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12808111	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1894075	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28513476	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34023835	1.00[ASN][1000 genomes]
rs34385073	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35455220	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35963948	1.00[ASN][1000 genomes]
rs4432047	1.00[ASN][1000 genomes]
rs6592517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67897720	1.00[ASN][1000 genomes]
rs7103650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114877	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7116594	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123808	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127013	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7127179	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127705	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7127940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7925481	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7925649	0.80[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs7930891	1.00[ASN][1000 genomes]
rs7942649	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs882904	1.00[ASN][1000 genomes]
rs9988805	1.00[JPT][hapmap];0.82[AMR][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	nsv832208	chr11:72876184-73091003	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv1821041	chr11:72937162-73113080	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12790863	PAAF1	cis	parietal	SCAN
rs12790863	KLHL35	cis	parietal	SCAN
rs12790863	FAM168A	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72975800-72980600	Weak transcription	Pancreas	Pancrea
2	chr11:72976200-72979800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:72976400-72981200	Enhancers	Placenta	Placenta
4	chr11:72976400-72984800	Enhancers	Placenta Amnion	Placenta Amnion
5	chr11:72976800-72980600	Enhancers	Fetal Intestine Large	intestine
6	chr11:72976800-72980800	Enhancers	Fetal Muscle Trunk	muscle
7	chr11:72977000-72981200	Weak transcription	A549	lung
8	chr11:72977000-72983200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:72977200-72991600	Weak transcription	Osteobl	bone
10	chr11:72977400-72981800	Enhancers	Fetal Muscle Leg	muscle
11	chr11:72977600-72980600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:72978000-72979800	Weak transcription	Left Ventricle	heart
13	chr11:72978000-72982800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:72978000-72986000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr11:72978400-72979800	Genic enhancers	Spleen	Spleen
16	chr11:72978600-72979800	Weak transcription	Right Atrium	heart
17	chr11:72978800-72982800	Weak transcription	HSMMtube	muscle
18	chr11:72979000-72980000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr11:72979000-72980400	Weak transcription	Right Ventricle	heart
20	chr11:72979000-72980600	Genic enhancers	Fetal Intestine Small	intestine
21	chr11:72979000-72981600	Enhancers	Lung	lung
22	chr11:72979000-72984200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr11:72979200-72980600	Weak transcription	Colonic Mucosa	Colon
24	chr11:72979200-72980600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr11:72979200-72980600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr11:72979200-72981800	Weak transcription	Fetal Heart	heart

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