Variant report

Variant	rs12193574
Chromosome Location	chr6:131225131-131225132
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs12526896	0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12530288	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12664445	0.87[ASN][1000 genomes]
rs2068147	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183967	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2275509	0.91[ASN][1000 genomes]
rs3777434	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs3777435	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs3777436	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs3777440	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777441	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777442	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777455	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777458	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs3777461	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777462	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777465	0.90[ASN][1000 genomes]
rs3777466	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3798249	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3798250	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3822861	0.93[ASN][1000 genomes]
rs3822863	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4323333	0.99[ASN][1000 genomes]
rs4357159	0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4897468	0.86[JPT][hapmap]
rs4897471	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897472	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4897474	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569707	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6569708	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs6569715	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6908917	0.83[CHD][hapmap]
rs6919007	0.90[JPT][hapmap]
rs6941712	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7742376	0.83[CHD][hapmap]
rs7760965	0.90[JPT][hapmap]
rs7763584	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7773290	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775013	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs9321257	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9321260	0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs933063	0.90[JPT][hapmap]
rs9375779	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9375781	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9375782	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9375783	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9375785	0.88[CHD][hapmap]
rs9375789	0.86[CHD][hapmap]
rs9388861	0.90[JPT][hapmap]
rs9388863	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs9388864	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9388869	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9398967	0.84[CHD][hapmap]
rs9402299	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9483185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9483192	0.97[ASN][1000 genomes]
rs9483201	0.80[ASN][1000 genomes]
rs9492755	0.91[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs9492756	0.89[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12193574	ALDH8A1	cis	cerebellum	SCAN
rs12193574	VNN3	cis	parietal	SCAN
rs12193574	EPB41L2	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131159000-131229000	Weak transcription	Colonic Mucosa	Colon
2	chr6:131190400-131227000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:131191000-131234400	Weak transcription	Esophagus	oesophagus
4	chr6:131191200-131233000	Weak transcription	Spleen	Spleen
5	chr6:131203600-131234200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:131204400-131228600	Weak transcription	Stomach Mucosa	stomach
7	chr6:131209000-131234000	Weak transcription	Fetal Thymus	thymus
8	chr6:131209800-131228000	Weak transcription	HUVEC	blood vessel
9	chr6:131211000-131228400	Weak transcription	Small Intestine	intestine
10	chr6:131211200-131234000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:131211400-131234200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:131213600-131232200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:131215000-131228800	Weak transcription	Liver	Liver
14	chr6:131215200-131234000	Weak transcription	Primary T cells from cord blood	blood
15	chr6:131215200-131234200	Weak transcription	Thymus	Thymus
16	chr6:131215400-131238200	Weak transcription	Aorta	Aorta
17	chr6:131215600-131228600	Weak transcription	Fetal Intestine Small	intestine
18	chr6:131215600-131233800	Weak transcription	Pancreas	Pancrea
19	chr6:131215800-131228400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:131216600-131233800	Weak transcription	Ovary	ovary
21	chr6:131216800-131226200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:131216800-131227800	Weak transcription	GM12878-XiMat	blood
23	chr6:131216800-131230200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:131218200-131228600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:131220600-131281200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:131220800-131228400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr6:131220800-131228600	Weak transcription	Fetal Intestine Large	intestine
28	chr6:131220800-131228800	Weak transcription	Brain Angular Gyrus	brain
29	chr6:131222200-131229200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr6:131222200-131229200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:131222200-131229200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:131222200-131230400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr6:131222200-131234000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr6:131222200-131234200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:131222200-131234400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:131222200-131236400	Weak transcription	Fetal Lung	lung
37	chr6:131222200-131248400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:131222200-131251800	Weak transcription	Primary B cells from cord blood	blood
39	chr6:131222400-131226000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:131222400-131227000	Weak transcription	HMEC	breast
41	chr6:131222400-131228600	Weak transcription	HepG2	liver
42	chr6:131222400-131228800	Weak transcription	Brain Hippocampus Middle	brain
43	chr6:131222400-131229000	Weak transcription	Brain Substantia Nigra	brain
44	chr6:131222400-131229000	Weak transcription	Fetal Muscle Leg	muscle
45	chr6:131222400-131229000	Weak transcription	Left Ventricle	heart
46	chr6:131222400-131229200	Weak transcription	Brain Anterior Caudate	brain
47	chr6:131222400-131232800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr6:131222400-131233200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:131222400-131233200	Weak transcription	HSMMtube	muscle
50	chr6:131222400-131233800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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