Variant report

Variant	rs11046858
Chromosome Location	chr12:8854725-8854726
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:8849809..8853868-chr12:8853971..8860490,9	MCF-7	breast:
2	chr12:8853948..8856246-chr12:8860962..8863055,2	K562	blood:
3	chr12:8850295..8852677-chr12:8853154..8857023,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166532	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10082771	1.00[ASN][1000 genomes]
rs10128818	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10505736	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10842109	1.00[ASN][1000 genomes]
rs10842131	1.00[ASN][1000 genomes]
rs11046766	1.00[ASN][1000 genomes]
rs11046832	1.00[ASN][1000 genomes]
rs11046872	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11046887	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11046900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047068	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612882	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11616092	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12296571	0.92[ASN][1000 genomes]
rs12296587	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12296895	1.00[ASN][1000 genomes]
rs12297411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12299708	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300013	1.00[ASN][1000 genomes]
rs12302099	1.00[JPT][hapmap]
rs12303273	1.00[JPT][hapmap]
rs12303275	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12304092	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304853	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306245	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12306562	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12307610	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309618	0.90[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12312128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314360	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12314822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316311	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12318215	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16917739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16917746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302488	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35146959	1.00[ASN][1000 genomes]
rs3858672	1.00[ASN][1000 genomes]
rs56094803	1.00[ASN][1000 genomes]
rs56113263	1.00[ASN][1000 genomes]
rs56387756	1.00[ASN][1000 genomes]
rs56837371	1.00[ASN][1000 genomes]
rs56878267	1.00[ASN][1000 genomes]
rs57676185	1.00[ASN][1000 genomes]
rs57747511	1.00[ASN][1000 genomes]
rs58333563	0.83[ASN][1000 genomes]
rs58451473	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58503001	0.83[ASN][1000 genomes]
rs58544193	0.83[ASN][1000 genomes]
rs58612925	1.00[ASN][1000 genomes]
rs58732156	1.00[ASN][1000 genomes]
rs58863166	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58866787	1.00[ASN][1000 genomes]
rs58998046	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59235894	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59306936	1.00[ASN][1000 genomes]
rs59562279	1.00[ASN][1000 genomes]
rs59566766	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59750351	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59824700	1.00[ASN][1000 genomes]
rs59935835	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60048072	1.00[ASN][1000 genomes]
rs60224353	1.00[ASN][1000 genomes]
rs60331702	1.00[ASN][1000 genomes]
rs60932450	1.00[ASN][1000 genomes]
rs61054720	1.00[ASN][1000 genomes]
rs61101189	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61187268	1.00[ASN][1000 genomes]
rs61395640	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61431903	1.00[ASN][1000 genomes]
rs61450603	1.00[ASN][1000 genomes]
rs6487313	1.00[JPT][hapmap]
rs6487333	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6487347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487353	1.00[ASN][1000 genomes]
rs6487354	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487361	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7132012	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7136480	1.00[ASN][1000 genomes]
rs7139182	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7299203	1.00[ASN][1000 genomes]
rs73036906	1.00[ASN][1000 genomes]
rs7303757	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7307494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313569	1.00[CEU][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313580	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74059963	1.00[ASN][1000 genomes]
rs74059966	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74059968	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74059969	1.00[ASN][1000 genomes]
rs74059978	1.00[ASN][1000 genomes]
rs74059985	1.00[ASN][1000 genomes]
rs74059990	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs74059992	1.00[ASN][1000 genomes]
rs74061803	1.00[ASN][1000 genomes]
rs74061818	1.00[ASN][1000 genomes]
rs7954527	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955163	1.00[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960582	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7961340	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964869	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7968935	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7972763	1.00[ASN][1000 genomes]
rs7973476	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975293	1.00[ASN][1000 genomes]
rs7975977	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977372	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11046858	FERMT1	trans	lymphoblastoid	seeQTL
rs11046858	CD2	trans	lymphoblastoid	seeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8851400-8862000	Weak transcription	Gastric	stomach
2	chr12:8851600-8855600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:8851600-8862000	Weak transcription	Lung	lung
4	chr12:8851800-8855600	Weak transcription	Brain Angular Gyrus	brain
5	chr12:8851800-8859800	Weak transcription	Spleen	Spleen
6	chr12:8851800-8862000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:8851800-8862000	Weak transcription	Left Ventricle	heart
8	chr12:8851800-8862000	Weak transcription	HSMM	muscle
9	chr12:8851800-8862000	Weak transcription	HSMMtube	muscle
10	chr12:8851800-8863400	Weak transcription	Right Ventricle	heart
11	chr12:8851800-8873200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr12:8851800-8877200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:8852000-8855000	Enhancers	Fetal Brain Male	brain
14	chr12:8852000-8855200	Weak transcription	Fetal Kidney	kidney
15	chr12:8852000-8861800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:8852400-8859600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:8852600-8855000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:8852600-8862000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:8852600-8874600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:8852600-8880000	Weak transcription	HMEC	breast
21	chr12:8852800-8859800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:8852800-8863800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr12:8852800-8864200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:8852800-8871400	Weak transcription	Fetal Intestine Large	intestine
25	chr12:8852800-8877200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:8852800-8908600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr12:8853000-8854800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:8853000-8855800	Enhancers	Colon Smooth Muscle	Colon
29	chr12:8853000-8862000	Weak transcription	Primary T cells from cord blood	blood
30	chr12:8853000-8871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:8853000-8873200	Weak transcription	A549	lung
32	chr12:8853000-8875600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:8853200-8854800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:8853200-8855000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr12:8853200-8855200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr12:8853200-8855600	Enhancers	Adipose Nuclei	Adipose
37	chr12:8853200-8855800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:8853200-8856200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:8853200-8859800	Weak transcription	Fetal Intestine Small	intestine
40	chr12:8853200-8861200	Weak transcription	HUVEC	blood vessel
41	chr12:8853200-8861200	Weak transcription	Osteobl	bone
42	chr12:8853200-8861600	Weak transcription	NHDF-Ad	bronchial
43	chr12:8853200-8862000	Weak transcription	Fetal Thymus	thymus
44	chr12:8853200-8862000	Weak transcription	Psoas Muscle	Psoas
45	chr12:8853200-8868400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr12:8853200-8872400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr12:8853200-8934000	Weak transcription	K562	blood
48	chr12:8853400-8854800	Active TSS	Aorta	Aorta
49	chr12:8853400-8855800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:8853400-8859400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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