Variant report

Variant	rs4615534
Chromosome Location	chr8:38955568-38955569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:38895697..38898348-chr8:38953067..38955793,2	K562	blood:
2	chr8:38949535..38951881-chr8:38954038..38956158,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10089487	0.82[MEX][hapmap]
rs10092021	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10093975	0.82[ASW][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.91[YRI][hapmap]
rs10441608	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10809000	0.82[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10809001	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11784624	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11985898	0.82[CEU][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12156418	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28434452	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28563781	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28564878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28579045	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28690874	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28868044	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4075849	1.00[CEU][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4269506	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4517088	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4733904	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4733971	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55797573	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56018450	0.80[AMR][1000 genomes]
rs59118660	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59814883	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6474517	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6474525	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67200247	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6991383	1.00[ASW][hapmap];0.82[CEU][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6991968	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs6997721	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7001985	0.86[YRI][hapmap]
rs7006535	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7013358	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7015505	1.00[ASW][hapmap];0.85[CEU][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7464810	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7818363	0.85[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7821437	0.85[CEU][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7823125	0.87[ASW][hapmap];0.81[JPT][hapmap]
rs7830975	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7831735	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs7832284	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7832578	0.81[CHD][hapmap]
rs7834967	0.82[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7835604	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7836422	0.87[ASW][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap]
rs7840044	1.00[ASW][hapmap];0.82[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7840270	0.82[JPT][hapmap];0.86[MEX][hapmap]
rs7844927	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9650347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4615534	PLEKHA2	cis	lymphoblastoid	seeQTL
rs4615534	TM2D2	cis	parietal	SCAN
rs4615534	ADAM32	cis	Artery Tibial	GTEx
rs4615534	HTRA4	cis	multi-tissue	Pritchard
rs4615534	ADAM32	cis	Nerve Tibial	GTEx
rs4615534	ADAM32	cis	Adipose Subcutaneous	GTEx
rs4615534	ADAM32	cis	Thyroid	GTEx
rs4615534	ADAM32	cis	Artery Aorta	GTEx
rs4615534	TM2D2	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

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	chr8:38935800-38958800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr8:38939200-38964800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr8:38941400-38960000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr8:38941600-38956200	Weak transcription	GM12878-XiMat	blood
23	chr8:38941600-38960600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr8:38941600-38964800	Weak transcription	Psoas Muscle	Psoas
25	chr8:38944600-38965000	Weak transcription	Esophagus	oesophagus
26	chr8:38945200-38964800	Weak transcription	Fetal Heart	heart
27	chr8:38946600-38964800	Weak transcription	Small Intestine	intestine
28	chr8:38946800-38964800	Weak transcription	Fetal Intestine Small	intestine
29	chr8:38946800-38964800	Weak transcription	Stomach Mucosa	stomach
30	chr8:38947800-38965000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr8:38949000-38959800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr8:38949400-38964600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr8:38949400-38964800	Weak transcription	Brain Angular Gyrus	brain
34	chr8:38949600-38957600	Weak transcription	Fetal Muscle Leg	muscle
35	chr8:38949600-38958000	Weak transcription	Left Ventricle	heart
36	chr8:38949600-38958000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr8:38949600-38958200	Weak transcription	Spleen	Spleen
38	chr8:38949600-38958400	Weak transcription	NHEK	skin
39	chr8:38949600-38958800	Weak transcription	Ovary	ovary
40	chr8:38949600-38959200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr8:38949600-38959400	Weak transcription	Adipose Nuclei	Adipose
42	chr8:38949600-38959400	Weak transcription	Liver	Liver
43	chr8:38949600-38959600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr8:38949600-38959800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr8:38949600-38960200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr8:38949600-38960600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr8:38949600-38960600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr8:38949600-38963600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr8:38949600-38964200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr8:38949600-38964600	Weak transcription	Aorta	Aorta

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