Variant report

Variant	rs9996883
Chromosome Location	chr4:54357177-54357178
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:54357078..54357883-chr4:54467415..54468360,4	MCF-7	breast:
2	chr4:54353594..54355161-chr4:54356979..54358658,2	MCF-7	breast:
3	chr4:54355457..54358448-chr4:54362389..54364275,2	K562	blood:

Variant related genes	Relation type
ENSG00000250930	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10000746	0.83[CHB][hapmap]
rs10001201	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10005424	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10007903	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10011259	0.81[CEU][hapmap]
rs10011394	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021541	0.81[ASN][1000 genomes]
rs10028142	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10032903	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1021099	0.80[ASN][1000 genomes]
rs11133276	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11722866	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11723755	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11725230	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11734039	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs11734681	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11947256	0.83[ASN][1000 genomes]
rs12507563	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12507739	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12508701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511088	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12511253	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12642403	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12651390	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs13150384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471597	0.80[ASN][1000 genomes]
rs1481819	0.82[CEU][hapmap]
rs1481824	0.82[CEU][hapmap]
rs1531748	0.86[CEU][hapmap]
rs17082893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17082923	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17520800	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2090117	0.82[CEU][hapmap]
rs2271558	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2271559	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2412447	0.82[CEU][hapmap];0.81[ASN][1000 genomes]
rs2412488	0.82[CEU][hapmap]
rs28414913	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28459503	0.81[ASN][1000 genomes]
rs35089837	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35499169	0.81[ASN][1000 genomes]
rs35978987	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36011216	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3765158	0.82[CEU][hapmap]
rs3811785	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4864760	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs4864767	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56998298	0.80[ASN][1000 genomes]
rs57297394	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6554104	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6554105	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs6554106	0.82[CEU][hapmap]
rs6818788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6822201	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6825364	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6828559	0.91[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs6832626	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6833766	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6838260	0.94[ASW][hapmap];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[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839922	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6840343	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6840530	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6843529	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6848887	0.81[ASN][1000 genomes]
rs7655975	0.81[ASN][1000 genomes]
rs7682199	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7686876	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7688853	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689981	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7690908	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7691578	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7691892	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7697622	0.81[ASN][1000 genomes]
rs7698792	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs931181	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.80[ASN][1000 genomes]
rs931182	0.82[CEU][hapmap]
rs9312639	0.90[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap]
rs9995284	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9996883	LYRM5	trans	cerebellum	SCAN
rs9996883	PIGW	trans	cerebellum	SCAN
rs9996883	EXOC1	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54327800-54362200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr4:54328200-54362000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:54328400-54362000	Weak transcription	Brain Angular Gyrus	brain
4	chr4:54329600-54373600	Weak transcription	Brain Germinal Matrix	brain
5	chr4:54329800-54374000	Weak transcription	Left Ventricle	heart
6	chr4:54333000-54363600	Weak transcription	Aorta	Aorta
7	chr4:54333000-54374800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:54342800-54360600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:54343000-54385600	Weak transcription	Fetal Brain Female	brain
10	chr4:54343200-54376800	Weak transcription	Brain Anterior Caudate	brain
11	chr4:54343400-54363000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:54343600-54364600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:54346400-54374000	Weak transcription	Right Ventricle	heart
14	chr4:54347600-54401800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr4:54348000-54362200	Weak transcription	Fetal Intestine Large	intestine
16	chr4:54348200-54359600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:54349000-54360000	Weak transcription	Liver	Liver
18	chr4:54352800-54361800	Weak transcription	Fetal Intestine Small	intestine
19	chr4:54352800-54362000	Weak transcription	Esophagus	oesophagus
20	chr4:54353400-54357400	Weak transcription	Ovary	ovary
21	chr4:54353600-54362000	Weak transcription	Gastric	stomach
22	chr4:54353600-54362000	Weak transcription	Pancreas	Pancrea
23	chr4:54354600-54358000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:54355000-54357800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:54355000-54357800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr4:54355000-54357800	Enhancers	Osteobl	bone
27	chr4:54355200-54378600	Weak transcription	Fetal Brain Male	brain
28	chr4:54355400-54357400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr4:54355400-54357600	Enhancers	NH-A	brain
30	chr4:54355600-54357200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:54356400-54357200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:54356400-54357200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:54356400-54357200	Flanking Active TSS	NHDF-Ad	bronchial
34	chr4:54356400-54357800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:54356400-54357800	Enhancers	HSMMtube	muscle
36	chr4:54356600-54357400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:54356600-54357600	Enhancers	H1 Cell Line	embryonic stem cell
38	chr4:54356600-54357800	Enhancers	Fetal Lung	lung
39	chr4:54356600-54357800	Enhancers	Fetal Stomach	stomach
40	chr4:54356600-54373400	Weak transcription	Right Atrium	heart
41	chr4:54356800-54357200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr4:54356800-54357200	Flanking Active TSS	NHLF	lung
43	chr4:54356800-54357400	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr4:54356800-54357600	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr4:54356800-54357600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr4:54356800-54357600	Weak transcription	Fetal Muscle Leg	muscle
47	chr4:54356800-54357600	Weak transcription	Placenta	Placenta
48	chr4:54356800-54357800	Enhancers	Adipose Nuclei	Adipose
49	chr4:54356800-54357800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr4:54356800-54362400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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