Variant report

Variant	rs2293671
Chromosome Location	chr2:20137864-20137865
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20099362..20101593-chr2:20136841..20138803,2	MCF-7	breast:
2	chr2:20136412..20138725-chr2:20188687..20190827,2	MCF-7	breast:
3	chr2:20136956..20138570-chr2:20139864..20142025,2	K562	blood:
4	chr2:20101371..20103225-chr2:20137366..20140099,2	K562	blood:

Variant related genes	Relation type
ENSG00000118965	Chromatin interaction
ENSG00000183891	Chromatin interaction
ENSG00000271991	Chromatin interaction
ENSG00000227210	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10169398	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175095	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10197385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10208878	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495701	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1060742	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11096632	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]
rs11888045	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11889206	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12052274	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12613209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12620863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13415707	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[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];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16987265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs28477921	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28502265	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35957485	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109404	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109406	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109413	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109415	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109416	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109418	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109419	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109420	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109421	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6707471	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719397	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755153	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563410	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7572167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7589478	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594214	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2293671	TTC32	cis	Stomach	GTEx
rs2293671	TTC32	cis	lung	GTEx
rs2293671	TTC32	cis	Thyroid	GTEx
rs2293671	TTC32	Cis_1M	lymphoblastoid	RTeQTL
rs2293671	LOC130502	cis	multi-tissue	Pritchard
rs2293671	TTC32	cis	Esophagus Muscularis	GTEx
rs2293671	TTC32	cis	Lymphoblastoid	GTEx
rs2293671	TTC32	cis	parietal	SCAN
rs2293671	MYCN	cis	parietal	SCAN
rs2293671	TTC32	cis	Adipose Subcutaneous	GTEx
rs2293671	TTC32	cis	cerebellum	SCAN
rs2293671	TTC32	cis	lymphoblastoid	seeQTL
rs2293671	TTC32	cis	Esophagus Mucosa	GTEx
rs2293671	TTC32	cis	multi-tissue	Pritchard
rs2293671	TTC32	cis	Heart Left Ventricle	GTEx

Chromatin state (count:113 , 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	chr2:20114400-20143800	Weak transcription	Brain Substantia Nigra	brain
3	chr2:20117600-20188400	Weak transcription	Brain Angular Gyrus	brain
4	chr2:20124800-20142800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:20127400-20167800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:20127600-20139200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:20128000-20139200	Weak transcription	Pancreas	Pancrea
8	chr2:20128400-20188400	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:20128400-20189200	Weak transcription	Small Intestine	intestine
10	chr2:20129400-20138600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:20129400-20143000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:20129400-20144000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:20129400-20184800	Weak transcription	Esophagus	oesophagus
14	chr2:20129600-20138000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:20129600-20149800	Weak transcription	Spleen	Spleen
16	chr2:20129600-20189000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:20130200-20189000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:20130400-20140200	Weak transcription	Liver	Liver
19	chr2:20130400-20141800	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:20130400-20142000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:20130400-20142600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:20130400-20149400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:20130400-20149400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:20130400-20164600	Weak transcription	Lung	lung
25	chr2:20130400-20188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:20130600-20138600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:20130600-20138800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:20130600-20139200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:20130600-20139800	Weak transcription	Fetal Stomach	stomach
30	chr2:20130600-20140000	Weak transcription	K562	blood
31	chr2:20130600-20142800	Weak transcription	Fetal Intestine Small	intestine
32	chr2:20130600-20143800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:20130600-20161200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:20130600-20188800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr2:20131800-20189000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:20133000-20138800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:20133600-20140800	Weak transcription	Hela-S3	cervix
38	chr2:20133600-20164800	Weak transcription	Gastric	stomach
39	chr2:20133600-20184800	Weak transcription	Psoas Muscle	Psoas
40	chr2:20133800-20151600	Weak transcription	Fetal Kidney	kidney
41	chr2:20133800-20173200	Weak transcription	NHEK	skin
42	chr2:20133800-20176800	Weak transcription	HMEC	breast
43	chr2:20134200-20138800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr2:20134200-20168600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:20134400-20146800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr2:20134600-20138600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:20134600-20148400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:20135000-20138200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:20135200-20138000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:20135200-20138000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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