Variant report

Variant	rs3822863
Chromosome Location	chr6:131250223-131250224
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:131250056..131252912-chr6:131253561..131255639,2	MCF-7	breast:
2	chr6:131245188..131247804-chr6:131249935..131252148,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs12193574	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]
rs12526896	0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs12530288	0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs12664445	0.89[ASN][1000 genomes]
rs17180687	0.88[MKK][hapmap]
rs2068147	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2183967	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2275509	0.94[ASN][1000 genomes]
rs3777434	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs3777435	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs3777436	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs3777440	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777441	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777442	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777458	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs3777461	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777462	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777465	0.90[ASN][1000 genomes]
rs3777466	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3798249	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3798250	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3822861	0.90[ASN][1000 genomes]
rs4323333	0.96[ASN][1000 genomes]
rs4357159	0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs4897468	0.81[CHB][hapmap]
rs4897471	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4897472	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4897473	0.86[MKK][hapmap]
rs4897474	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4897484	0.86[MKK][hapmap]
rs6569707	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs6569708	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs6569715	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908917	0.84[CHD][hapmap]
rs6919007	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs6941712	0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs7742376	0.84[CHD][hapmap]
rs7760965	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs7763584	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7773290	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7775013	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs9321257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321260	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs933063	0.82[JPT][hapmap]
rs9375779	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375782	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9375783	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9375785	0.84[CHD][hapmap]
rs9375789	0.83[CHD][hapmap]
rs9388861	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9388863	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs9388864	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9388869	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9398967	0.81[CHD][hapmap]
rs9402292	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9402299	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9483185	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9483192	1.00[ASN][1000 genomes]
rs9483201	0.80[ASN][1000 genomes]
rs9492755	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9492756	0.92[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3822863	ALDH8A1	cis	cerebellum	SCAN
rs3822863	EPB41L2	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131220600-131281200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr6:131222200-131251800	Weak transcription	Primary B cells from cord blood	blood
3	chr6:131234000-131250600	Weak transcription	Fetal Stomach	stomach
4	chr6:131234800-131254000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:131234800-131266600	Weak transcription	GM12878-XiMat	blood
6	chr6:131236400-131254000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:131239200-131252600	Weak transcription	Dnd41	blood
8	chr6:131240000-131253600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:131242600-131254800	Weak transcription	Fetal Kidney	kidney
10	chr6:131242800-131255000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:131244200-131279000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:131244800-131255000	Weak transcription	Lung	lung
13	chr6:131245000-131254000	Weak transcription	Left Ventricle	heart
14	chr6:131245000-131254800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:131245400-131253600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:131246200-131252200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:131246200-131254200	Weak transcription	Fetal Intestine Large	intestine
18	chr6:131246200-131264800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:131246600-131254800	Weak transcription	Placenta	Placenta
20	chr6:131246800-131251200	Enhancers	Brain Angular Gyrus	brain
21	chr6:131247800-131254200	Weak transcription	Fetal Intestine Small	intestine
22	chr6:131248600-131251200	Enhancers	Brain Cingulate Gyrus	brain
23	chr6:131248800-131253800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:131248800-131254200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:131248800-131255000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr6:131249000-131250800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr6:131249000-131251200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr6:131249000-131252600	Weak transcription	HepG2	liver
29	chr6:131249000-131254200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:131249000-131254800	Weak transcription	HMEC	breast
31	chr6:131249000-131259000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:131249200-131250800	Enhancers	Adipose Nuclei	Adipose
33	chr6:131249200-131251000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:131249200-131253600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:131249200-131253800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:131249200-131254000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:131249200-131255000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:131249400-131250600	Enhancers	Right Atrium	heart
39	chr6:131249400-131251200	Enhancers	Psoas Muscle	Psoas
40	chr6:131249400-131251200	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr6:131249600-131250800	Enhancers	Brain Hippocampus Middle	brain
42	chr6:131249600-131251200	Enhancers	Brain Substantia Nigra	brain
43	chr6:131249800-131250400	Flanking Active TSS	Fetal Lung	lung
44	chr6:131249800-131250800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:131249800-131250800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:131249800-131250800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:131249800-131250800	Flanking Active TSS	NHDF-Ad	bronchial
48	chr6:131249800-131251200	Enhancers	Colon Smooth Muscle	Colon
49	chr6:131249800-131251200	Enhancers	Fetal Muscle Leg	muscle
50	chr6:131249800-131255000	Weak transcription	Small Intestine	intestine

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