Variant report

Variant	rs12206057
Chromosome Location	chr6:131212517-131212518
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr6:131211363-131212540	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
EPB41L2	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1043596	0.88[JPT][hapmap]
rs11154610	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12110524	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194612	0.88[JPT][hapmap]
rs2275509	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3777438	0.89[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3777454	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3777457	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777458	0.84[CEU][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3822861	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4323333	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4357159	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6569713	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66773803	0.80[ASN][1000 genomes]
rs6938586	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6939358	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7747517	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867707	0.94[JPT][hapmap]
rs915172	0.94[JPT][hapmap]
rs9321260	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9321265	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs9483192	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9492755	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9492756	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9492767	0.88[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9492775	0.81[CHB][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12206057	ALDH8A1	cis	cerebellum	SCAN
rs12206057	EPB41L2	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131149400-131213200	Weak transcription	Pancreas	Pancrea
2	chr6:131151600-131216600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:131158200-131214400	Weak transcription	Lung	lung
4	chr6:131159000-131229000	Weak transcription	Colonic Mucosa	Colon
5	chr6:131168800-131214600	Weak transcription	Fetal Kidney	kidney
6	chr6:131170400-131217400	Weak transcription	Psoas Muscle	Psoas
7	chr6:131170600-131213800	Weak transcription	GM12878-XiMat	blood
8	chr6:131171200-131223200	Weak transcription	Right Ventricle	heart
9	chr6:131171400-131220200	Weak transcription	Fetal Brain Male	brain
10	chr6:131175000-131222400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:131175200-131214000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:131175600-131221600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:131179200-131214000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:131179400-131222400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:131179600-131215000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:131181400-131214400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:131185800-131214400	Weak transcription	Thymus	Thymus
18	chr6:131187000-131214400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:131187000-131223200	Weak transcription	Gastric	stomach
20	chr6:131187200-131216400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:131188200-131216400	Weak transcription	HSMMtube	muscle
22	chr6:131190400-131227000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:131190800-131224200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:131191000-131234400	Weak transcription	Esophagus	oesophagus
25	chr6:131191200-131224200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:131191200-131233000	Weak transcription	Spleen	Spleen
27	chr6:131191600-131214600	Weak transcription	Fetal Intestine Small	intestine
28	chr6:131194200-131222000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:131195800-131224200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:131198600-131224200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr6:131201000-131222400	Strong transcription	Dnd41	blood
32	chr6:131201800-131214400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr6:131201800-131222000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:131203600-131234200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:131203800-131214400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:131204200-131213200	Weak transcription	Ovary	ovary
37	chr6:131204200-131213800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr6:131204400-131214400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr6:131204400-131214800	Weak transcription	Placenta	Placenta
40	chr6:131204400-131228600	Weak transcription	Stomach Mucosa	stomach
41	chr6:131204600-131213200	Weak transcription	Aorta	Aorta
42	chr6:131204600-131213200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr6:131205200-131222000	Weak transcription	A549	lung
44	chr6:131205400-131213200	Weak transcription	Fetal Stomach	stomach
45	chr6:131205400-131214200	Weak transcription	Left Ventricle	heart
46	chr6:131206400-131212800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr6:131207600-131212800	Weak transcription	Fetal Muscle Leg	muscle
48	chr6:131208000-131222000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr6:131209000-131234000	Weak transcription	Fetal Thymus	thymus
50	chr6:131209200-131214000	Weak transcription	Brain Inferior Temporal Lobe	brain

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