Variant report

Variant	rs11096632
Chromosome Location	chr2:20144372-20144373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20138433..20141277-chr2:20142757..20144627,2	K562	blood:
2	chr2:20138877..20140913-chr2:20142589..20144773,2	MCF-7	breast:
3	chr2:20135593..20137706-chr2:20143869..20146190,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10169398	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175095	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10197385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10208878	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495701	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1060742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11888045	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11889206	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12052274	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12613209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12617761	0.80[AMR][1000 genomes]
rs12620863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13415707	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13421472	0.87[CEU][hapmap];0.87[JPT][hapmap]
rs1381817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16987265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs28477921	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28502265	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35957485	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109398	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs62109404	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109406	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109416	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109418	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109419	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109420	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109421	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62109426	1.00[AFR][1000 genomes]
rs6707471	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755153	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7572167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7589478	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594214	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
3	nsv521619	chr2:20098208-20150817	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv527453	chr2:20109061-20160209	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv1798392	chr2:20131079-20173255	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11096632	TTC32	cis	Thyroid	GTEx
rs11096632	TTC32	Cis_1M	lymphoblastoid	RTeQTL
rs11096632	TTC32	cis	Heart Left Ventricle	GTEx
rs11096632	TTC32	cis	lymphoblastoid	seeQTL
rs11096632	LOC130502	cis	multi-tissue	Pritchard
rs11096632	TTC32	cis	Adipose Subcutaneous	GTEx
rs11096632	TTC32	cis	multi-tissue	Pritchard
rs11096632	TTC32	cis	Esophagus Mucosa	GTEx
rs11096632	ARHGAP32	trans	lymphoblastoid	seeQTL
rs11096632	TTC32	cis	lung	GTEx
rs11096632	TTC32	cis	Stomach	GTEx
rs11096632	TTC32	cis	Esophagus Muscularis	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20102800-20173200	Weak transcription	Fetal Brain Male	brain
2	chr2:20117600-20188400	Weak transcription	Brain Angular Gyrus	brain
3	chr2:20127400-20167800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:20128400-20188400	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:20128400-20189200	Weak transcription	Small Intestine	intestine
6	chr2:20129400-20184800	Weak transcription	Esophagus	oesophagus
7	chr2:20129600-20149800	Weak transcription	Spleen	Spleen
8	chr2:20129600-20189000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:20130200-20189000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:20130400-20149400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:20130400-20149400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:20130400-20164600	Weak transcription	Lung	lung
13	chr2:20130400-20188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:20130600-20161200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:20130600-20188800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:20131800-20189000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:20133600-20164800	Weak transcription	Gastric	stomach
18	chr2:20133600-20184800	Weak transcription	Psoas Muscle	Psoas
19	chr2:20133800-20151600	Weak transcription	Fetal Kidney	kidney
20	chr2:20133800-20173200	Weak transcription	NHEK	skin
21	chr2:20133800-20176800	Weak transcription	HMEC	breast
22	chr2:20134200-20168600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:20134400-20146800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:20134600-20148400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:20136400-20148800	Weak transcription	HSMM	muscle
26	chr2:20136400-20150800	Weak transcription	Thymus	Thymus
27	chr2:20136400-20177000	Weak transcription	GM12878-XiMat	blood
28	chr2:20136400-20177200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:20136600-20149400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:20136600-20151600	Weak transcription	Brain Germinal Matrix	brain
31	chr2:20136600-20171200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr2:20136600-20177200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:20136800-20171400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:20136800-20188800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:20136800-20189000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:20137200-20149200	Weak transcription	HUVEC	blood vessel
37	chr2:20137600-20145000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr2:20137600-20147400	Weak transcription	NHLF	lung
39	chr2:20137600-20150000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr2:20137600-20161000	Weak transcription	HSMMtube	muscle
41	chr2:20137600-20165200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:20137800-20146800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:20137800-20152000	Weak transcription	Brain Anterior Caudate	brain
44	chr2:20137800-20161200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr2:20137800-20165000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr2:20138000-20145200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr2:20138000-20146000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:20138000-20149000	Weak transcription	Adipose Nuclei	Adipose
49	chr2:20138000-20165000	Weak transcription	Fetal Brain Female	brain
50	chr2:20138000-20177000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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