Variant report

Variant	rs11172156
Chromosome Location	chr12:57705853-57705854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57701803..57704165-chr12:57704746..57706326,2	MCF-7	breast:
2	chr12:57704289..57706468-chr12:57708550..57710916,2	MCF-7	breast:
3	chr12:57702958..57705932-chr12:57847921..57850927,4	K562	blood:
4	chr12:57696649..57699351-chr12:57704431..57706467,2	K562	blood:

Variant related genes	Relation type
ENSG00000139269	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10747777	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10747778	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10783818	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783819	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs10783820	0.91[EUR][1000 genomes]
rs10783823	0.82[EUR][1000 genomes]
rs10876976	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[ASN][1000 genomes]
rs10876980	0.81[ASN][1000 genomes]
rs11172160	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172165	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172169	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172170	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172177	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172190	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11172191	0.82[AMR][1000 genomes]
rs11609986	0.92[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs12296766	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12310220	0.92[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12579911	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs12812140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1798710	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs2063778	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs2280139	0.95[JPT][hapmap]
rs35032945	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3923885	0.96[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs4075325	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs4760192	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760193	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760236	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs4760308	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760348	0.96[CEU][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760356	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4760357	0.80[EUR][1000 genomes]
rs481196	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs491750	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs533975	0.96[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs537482	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs543410	0.96[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs560048	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs568793	0.80[JPT][hapmap]
rs575153	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs6581131	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[EUR][1000 genomes]
rs6581134	0.85[CHB][hapmap];0.98[GIH][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6581135	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6581136	0.96[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6581139	0.82[EUR][1000 genomes]
rs7132367	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs7133939	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7135142	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7298418	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7307059	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7309659	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7313824	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7314266	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7358684	0.90[EUR][1000 genomes]
rs7398058	0.96[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7486863	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7977908	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11172156	XRCC6BP1	cis	multi-tissue	Pritchard
rs11172156	DKFZP586D0919	cis	multi-tissue	Pritchard

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57662800-57706000	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr12:57670400-57707000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr12:57675400-57707000	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:57677600-57713000	Weak transcription	Stomach Mucosa	stomach
5	chr12:57678000-57713000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:57691000-57736200	Weak transcription	Right Atrium	heart
7	chr12:57693600-57743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:57693800-57713000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:57694000-57706200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:57694000-57709400	Weak transcription	Colonic Mucosa	Colon
11	chr12:57694000-57710000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:57694000-57713200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:57694000-57713200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr12:57694000-57780000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:57694200-57734000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:57694400-57732400	Weak transcription	Ovary	ovary
17	chr12:57694400-57735000	Weak transcription	Psoas Muscle	Psoas
18	chr12:57695200-57794600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:57696800-57715200	Weak transcription	Gastric	stomach
20	chr12:57697000-57726000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:57697000-57735400	Weak transcription	Right Ventricle	heart
22	chr12:57697200-57707200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr12:57697200-57734000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:57697200-57745000	Weak transcription	Lung	lung
25	chr12:57697400-57713000	Weak transcription	Fetal Lung	lung
26	chr12:57697400-57721400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:57699800-57762400	Weak transcription	Left Ventricle	heart
28	chr12:57700000-57712600	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:57700000-57717800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:57700000-57719800	Weak transcription	Fetal Kidney	kidney
31	chr12:57700000-57720000	Weak transcription	Fetal Intestine Large	intestine
32	chr12:57700000-57733800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr12:57700000-57736000	Weak transcription	Fetal Brain Male	brain
34	chr12:57700200-57709800	Weak transcription	Fetal Brain Female	brain
35	chr12:57700400-57721600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:57702600-57706200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:57703200-57713000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:57703400-57706200	Weak transcription	Hela-S3	cervix
39	chr12:57703400-57733800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr12:57703400-57734600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr12:57703400-57742000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:57703600-57706000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr12:57703600-57719000	Weak transcription	Primary B cells from peripheral blood	blood
44	chr12:57703800-57713400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:57703800-57720200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:57703800-57723400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:57703800-57725000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:57703800-57726600	Weak transcription	Colon Smooth Muscle	Colon
49	chr12:57704000-57706000	Weak transcription	Fetal Intestine Small	intestine
50	chr12:57704000-57706000	Weak transcription	Fetal Stomach	stomach

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