Variant report

Variant	rs4733905
Chromosome Location	chr8:38959498-38959499
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10089487	0.86[GIH][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap]
rs10113077	0.82[JPT][hapmap]
rs10958813	0.95[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11777149	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11777376	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11787126	1.00[CEU][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11985898	0.81[MEX][hapmap]
rs12056655	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];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12541095	0.81[ASN][1000 genomes]
rs12541231	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12543388	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12543921	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12546318	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12548006	0.86[ASW][hapmap];0.91[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12548416	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12548948	0.95[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12549232	0.90[MEX][hapmap];0.82[TSI][hapmap]
rs12549547	1.00[CEU][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13248324	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13256952	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13268394	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]
rs13274567	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34070223	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34138150	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34185462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35391544	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35534138	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4129095	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4236757	0.82[TSI][hapmap]
rs4495395	0.86[GIH][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs4543512	0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4733901	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4733970	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66925354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7832578	0.86[GIH][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap]
rs7838874	0.88[GIH][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap]
rs9643858	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9643902	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9643904	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9643906	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021581	chr8:38934014-39043954	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4733905	PLEKHA2	cis	lymphoblastoid	seeQTL
rs4733905	TM2D2	cis	cerebellum	SCAN
rs4733905	ADAM32	cis	cerebellum	SCAN
rs4733905	DDHD2	cis	cerebellum	SCAN
rs4733905	TM2D2	cis	parietal	SCAN
rs4733905	SGK196	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:38897400-38963400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:38905000-38960000	Weak transcription	HSMMtube	muscle
3	chr8:38911800-38964800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:38914400-38964800	Weak transcription	Fetal Kidney	kidney
5	chr8:38914800-38964800	Weak transcription	Colonic Mucosa	Colon
6	chr8:38918000-38962600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr8:38919000-38970400	Weak transcription	K562	blood
8	chr8:38919600-38964800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr8:38920600-38963200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr8:38920800-38964800	Weak transcription	Fetal Brain Male	brain
11	chr8:38921000-38964800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr8:38921000-38965000	Weak transcription	Gastric	stomach
13	chr8:38921600-38964800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr8:38926200-38963600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr8:38932400-38964800	Weak transcription	Brain Germinal Matrix	brain
16	chr8:38934000-38960800	Weak transcription	Colon Smooth Muscle	Colon
17	chr8:38935600-38960200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr8:38935600-38964800	Weak transcription	Brain Anterior Caudate	brain
19	chr8:38939200-38964800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr8:38941400-38960000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr8:38941600-38960600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr8:38941600-38964800	Weak transcription	Psoas Muscle	Psoas
23	chr8:38944600-38965000	Weak transcription	Esophagus	oesophagus
24	chr8:38945200-38964800	Weak transcription	Fetal Heart	heart
25	chr8:38946600-38964800	Weak transcription	Small Intestine	intestine
26	chr8:38946800-38964800	Weak transcription	Fetal Intestine Small	intestine
27	chr8:38946800-38964800	Weak transcription	Stomach Mucosa	stomach
28	chr8:38947800-38965000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr8:38949000-38959800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr8:38949400-38964600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr8:38949400-38964800	Weak transcription	Brain Angular Gyrus	brain
32	chr8:38949600-38959600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr8:38949600-38959800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr8:38949600-38960200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr8:38949600-38960600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr8:38949600-38960600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr8:38949600-38963600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr8:38949600-38964200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr8:38949600-38964600	Weak transcription	Aorta	Aorta
40	chr8:38949600-38964600	Weak transcription	Fetal Stomach	stomach
41	chr8:38949600-38964800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr8:38949600-38964800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr8:38949600-38964800	Weak transcription	Pancreas	Pancrea
44	chr8:38949600-38964800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr8:38949600-38964800	Weak transcription	Right Ventricle	heart
46	chr8:38949600-38964800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr8:38949600-38965000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr8:38949600-38965000	Weak transcription	Lung	lung
49	chr8:38949800-38964400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr8:38949800-38964800	Weak transcription	Brain Hippocampus Middle	brain

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