Variant report

Variant	rs10929322
Chromosome Location	chr2:234149702-234149703
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234148867..234150781-chr2:234159986..234161805,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085978	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10164737	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10165561	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10167613	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10178603	0.89[ASN][1000 genomes]
rs10186850	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10187752	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10187822	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10192579	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10192702	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10195395	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10196794	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10199278	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10203952	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10206299	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10210302	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1045100	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10929325	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10929326	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11679791	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11680089	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11680130	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11687982	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11688431	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11690131	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11694081	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12162308	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12692250	0.85[ASN][1000 genomes]
rs12692254	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12994971	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12994997	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13003866	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13009506	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13015823	0.82[JPT][hapmap]
rs13035837	0.83[JPT][hapmap]
rs13391356	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13411660	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13412102	0.85[ASN][1000 genomes]
rs13418066	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1441092	0.83[JPT][hapmap]
rs1596017	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2119505	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2241878	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241879	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2241880	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289472	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289474	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289477	0.90[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs28454240	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2880080	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34123137	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34701569	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35300242	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36001488	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3762588	0.83[JPT][hapmap]
rs3792106	0.81[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.86[ASN][1000 genomes]
rs3792108	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3792109	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3792111	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3792112	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3816234	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3828309	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55835501	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56049444	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56227616	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6431654	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6431660	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6431661	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6705964	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6708373	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6738490	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6745825	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6752107	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7559194	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10929322	ATG16L1	cis	cerebellum	SCAN
rs10929322	SCARNA5	cis	parietal	SCAN
rs10929322	B3GNT7	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234138000-234151200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:234138400-234151200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr2:234144600-234150400	Weak transcription	Esophagus	oesophagus
4	chr2:234145400-234150600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:234145600-234151400	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr2:234145600-234152000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:234145600-234153600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:234146000-234151200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr2:234147600-234151400	Enhancers	Primary B cells from peripheral blood	blood
10	chr2:234148400-234150400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:234148400-234151200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:234148400-234152200	Enhancers	Primary B cells from cord blood	blood
13	chr2:234148600-234150800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr2:234148600-234150800	Enhancers	Small Intestine	intestine
15	chr2:234148600-234151200	Enhancers	Fetal Thymus	thymus
16	chr2:234149000-234150000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:234149200-234149800	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr2:234149200-234150200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:234149200-234151400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr2:234149200-234151400	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr2:234149400-234149800	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr2:234149400-234149800	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr2:234149400-234149800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr2:234149400-234149800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr2:234149400-234149800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr2:234149400-234149800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr2:234149400-234149800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:234149400-234149800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr2:234149400-234149800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr2:234149400-234150000	Enhancers	Thymus	Thymus
31	chr2:234149400-234150600	Weak transcription	Placenta	Placenta
32	chr2:234149400-234150600	Weak transcription	Spleen	Spleen
33	chr2:234149400-234151000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:234149400-234151000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:234149400-234151200	Enhancers	NHEK	skin
36	chr2:234149400-234152600	Enhancers	Stomach Mucosa	stomach
37	chr2:234149400-234153600	Enhancers	K562	blood
38	chr2:234149600-234149800	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr2:234149600-234149800	Enhancers	NH-A	brain
40	chr2:234149600-234150000	Flanking Active TSS	GM12878-XiMat	blood
41	chr2:234149600-234150600	Enhancers	Duodenum Mucosa	Duodenum
42	chr2:234149600-234150800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:234149600-234150800	Enhancers	HMEC	breast

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