Variant report

Variant	rs13268394
Chromosome Location	chr8:38875649-38875650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10086693	0.81[EUR][1000 genomes]
rs10089487	0.86[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs10106085	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs10113077	0.81[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs10958813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777149	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11777376	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11787126	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11985898	0.81[MEX][hapmap]
rs12056655	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];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12541231	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12543921	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12546318	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12548006	0.86[ASW][hapmap];0.87[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12548948	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12549232	0.90[MEX][hapmap];0.82[TSI][hapmap]
rs12549547	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13248324	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13256952	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13274567	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13282047	0.84[EUR][1000 genomes]
rs34138150	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34185462	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35391544	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35534138	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4128871	0.81[EUR][1000 genomes]
rs4129095	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4236757	0.82[TSI][hapmap]
rs4495395	0.81[CHB][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs4543512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4733897	0.81[JPT][hapmap]
rs4733901	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4733905	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4733964	0.81[JPT][hapmap]
rs4733970	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6474516	0.81[JPT][hapmap]
rs66925354	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7821237	0.81[EUR][1000 genomes]
rs7832578	0.81[CHB][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7838874	0.81[CHB][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs9643858	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9643902	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9643904	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9643906	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13268394	SGK196	cis	parietal	SCAN
rs13268394	TM2D2	cis	parietal	SCAN
rs13268394	DDHD2	cis	cerebellum	SCAN
rs13268394	TM2D2	cis	cerebellum	SCAN
rs13268394	ADAM32	cis	cerebellum	SCAN
rs13268394	PLEKHA2	cis	lymphoblastoid	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:38855800-38881600	Weak transcription	Fetal Kidney	kidney
2	chr8:38856600-38889600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:38856800-38889600	Weak transcription	Colonic Mucosa	Colon
4	chr8:38857200-38881400	Weak transcription	Fetal Brain Female	brain
5	chr8:38862600-38884400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr8:38862800-38878200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr8:38863400-38883200	Weak transcription	Brain Germinal Matrix	brain
8	chr8:38863600-38881000	Weak transcription	Small Intestine	intestine
9	chr8:38865000-38880600	Weak transcription	Brain Substantia Nigra	brain
10	chr8:38865000-38881400	Weak transcription	Spleen	Spleen
11	chr8:38865000-38887200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr8:38865000-38889600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr8:38865200-38877800	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr8:38865200-38887400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr8:38865400-38877200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr8:38865400-38886000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr8:38865400-38887800	Strong transcription	HSMM	muscle
18	chr8:38865400-38888800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr8:38865600-38888200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr8:38865600-38889000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr8:38866000-38888400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr8:38867000-38880400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr8:38868200-38881200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr8:38869000-38877600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr8:38869600-38902800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr8:38869800-38877400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr8:38869800-38880200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr8:38869800-38880200	Weak transcription	Lung	lung
29	chr8:38869800-38881400	Weak transcription	Right Ventricle	heart
30	chr8:38869800-38883200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr8:38869800-38885200	Weak transcription	Aorta	Aorta
32	chr8:38869800-38888400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr8:38870000-38879200	Weak transcription	Liver	Liver
34	chr8:38870000-38881200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr8:38870000-38881800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr8:38870000-38886400	Weak transcription	Pancreas	Pancrea
37	chr8:38871000-38877600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr8:38871600-38876600	Genic enhancers	A549	lung
39	chr8:38871600-38877600	Strong transcription	Primary hematopoietic stem cells	blood
40	chr8:38872000-38886200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr8:38872000-38890400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr8:38872200-38875800	Strong transcription	GM12878-XiMat	blood
43	chr8:38872200-38877800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr8:38872400-38881400	Strong transcription	HMEC	breast
45	chr8:38872400-38888200	Strong transcription	Fetal Intestine Large	intestine
46	chr8:38872600-38876600	Weak transcription	Stomach Mucosa	stomach
47	chr8:38872600-38889600	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr8:38872600-38889800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr8:38872800-38888000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr8:38873200-38883800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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