Variant report

Variant	rs4517088
Chromosome Location	chr8:38964647-38964648
allele	A/G
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	POLR2A	chr8:38963530-38966569	A549	lung:	n/a	n/a
2	POLR2A	chr8:38963971-38965210	HepG2	liver:	n/a	n/a
3	POLR2A	chr8:38964195-38966666	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr8:38963444-38965828	K562	blood:	n/a	n/a
5	CTCF	chr8:38964640-38964790	NHDF-neo	bronchial:	n/a	n/a

Variant related genes	Relation type
ADAM32	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10089487	0.83[MEX][hapmap]
rs10092021	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10093975	0.82[ASW][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.91[YRI][hapmap]
rs10441608	1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10809000	0.82[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10809001	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11784624	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11985898	0.82[CEU][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12156418	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28434452	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28563781	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28564878	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28579045	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28690874	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28868044	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4075849	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4269506	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4615534	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	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4733971	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55797573	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59118660	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59814883	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6474517	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6474525	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67200247	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6991383	1.00[ASW][hapmap];0.82[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6991968	0.86[JPT][hapmap];0.83[MEX][hapmap]
rs6997721	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7001985	0.81[JPT][hapmap];0.86[YRI][hapmap]
rs7006535	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7013358	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7015505	1.00[ASW][hapmap];0.85[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7464810	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7818363	0.85[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7821437	0.85[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7823125	0.87[ASW][hapmap];0.85[JPT][hapmap]
rs7830975	0.83[EUR][1000 genomes]
rs7831735	0.86[JPT][hapmap];0.83[MEX][hapmap]
rs7832284	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7834967	0.82[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7835604	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7836422	0.87[ASW][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap]
rs7840044	1.00[ASW][hapmap];0.82[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7840270	0.86[JPT][hapmap];0.86[MEX][hapmap]
rs7844927	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9650347	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4517088	ADAM32	cis	Artery Tibial	GTEx
rs4517088	TM2D2	cis	parietal	SCAN
rs4517088	ADAM32	cis	Nerve Tibial	GTEx
rs4517088	ADAM32	cis	Thyroid	GTEx
rs4517088	ADAM32	cis	Adipose Subcutaneous	GTEx
rs4517088	ADAM32	cis	Artery Aorta	GTEx
rs4517088	TM2D2	cis	cerebellum	SCAN
rs4517088	PLEKHA2	cis	lymphoblastoid	seeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:38911800-38964800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:38914400-38964800	Weak transcription	Fetal Kidney	kidney
3	chr8:38914800-38964800	Weak transcription	Colonic Mucosa	Colon
4	chr8:38919000-38970400	Weak transcription	K562	blood
5	chr8:38919600-38964800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr8:38920800-38964800	Weak transcription	Fetal Brain Male	brain
7	chr8:38921000-38964800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr8:38921000-38965000	Weak transcription	Gastric	stomach
9	chr8:38921600-38964800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr8:38932400-38964800	Weak transcription	Brain Germinal Matrix	brain
11	chr8:38935600-38964800	Weak transcription	Brain Anterior Caudate	brain
12	chr8:38939200-38964800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr8:38941600-38964800	Weak transcription	Psoas Muscle	Psoas
14	chr8:38944600-38965000	Weak transcription	Esophagus	oesophagus
15	chr8:38945200-38964800	Weak transcription	Fetal Heart	heart
16	chr8:38946600-38964800	Weak transcription	Small Intestine	intestine
17	chr8:38946800-38964800	Weak transcription	Fetal Intestine Small	intestine
18	chr8:38946800-38964800	Weak transcription	Stomach Mucosa	stomach
19	chr8:38947800-38965000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr8:38949400-38964800	Weak transcription	Brain Angular Gyrus	brain
21	chr8:38949600-38964800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr8:38949600-38964800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr8:38949600-38964800	Weak transcription	Pancreas	Pancrea
24	chr8:38949600-38964800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr8:38949600-38964800	Weak transcription	Right Ventricle	heart
26	chr8:38949600-38964800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr8:38949600-38965000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr8:38949600-38965000	Weak transcription	Lung	lung
29	chr8:38949800-38964800	Weak transcription	Brain Hippocampus Middle	brain
30	chr8:38950000-38964800	Weak transcription	Brain Substantia Nigra	brain
31	chr8:38951400-38964800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr8:38955600-38964800	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr8:38957000-38964800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr8:38959000-38964800	Weak transcription	Ovary	ovary
35	chr8:38959800-38965200	Strong transcription	A549	lung
36	chr8:38960800-38964800	Weak transcription	NHEK	skin
37	chr8:38961000-38964800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr8:38961000-38965000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr8:38961000-38966200	Weak transcription	HepG2	liver
40	chr8:38961200-38964800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr8:38961200-38964800	Weak transcription	Left Ventricle	heart
42	chr8:38961200-38970200	Weak transcription	HMEC	breast
43	chr8:38961400-38964800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr8:38961400-38964800	Weak transcription	Fetal Intestine Large	intestine
45	chr8:38961400-38964800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr8:38961400-38965200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr8:38961600-38964800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr8:38961600-38964800	Weak transcription	Colon Smooth Muscle	Colon
49	chr8:38961600-38964800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr8:38961600-38964800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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