Variant report

Variant	rs7625821
Chromosome Location	chr3:51513236-51513237
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	chr3:51512991..51515016-chr3:51519404..51520955,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1031925	1.00[CEU][hapmap]
rs11130286	0.90[CHB][hapmap];0.84[CHD][hapmap];0.87[MEX][hapmap]
rs11130290	0.90[CHB][hapmap];0.84[CHD][hapmap];0.87[MEX][hapmap]
rs11130293	0.81[EUR][1000 genomes]
rs11706571	0.90[CHB][hapmap];0.84[CHD][hapmap];0.87[MEX][hapmap]
rs11709482	0.81[AMR][1000 genomes]
rs11719995	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11721253	0.81[EUR][1000 genomes]
rs11917683	1.00[CEU][hapmap]
rs12632046	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1318649	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs1383251	1.00[CEU][hapmap]
rs1480353	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1542574	0.88[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs1552074	0.92[CEU][hapmap]
rs17051762	0.91[CEU][hapmap]
rs2127655	0.92[CEU][hapmap]
rs2164599	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2219890	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2219891	0.90[CHB][hapmap];0.84[CHD][hapmap];0.87[MEX][hapmap]
rs2241784	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4234644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs4355273	0.85[CEU][hapmap]
rs4687721	1.00[CEU][hapmap]
rs4687800	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4974104	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4974105	1.00[CEU][hapmap]
rs4974108	0.90[CHB][hapmap];0.84[CHD][hapmap];0.87[MEX][hapmap]
rs6445601	0.90[CHB][hapmap];0.84[CHD][hapmap];0.87[MEX][hapmap]
rs6445604	0.90[CHB][hapmap];0.84[CHD][hapmap];0.87[MEX][hapmap]
rs6445611	0.90[CHB][hapmap];0.85[CHD][hapmap];0.87[MEX][hapmap]
rs6445620	1.00[CEU][hapmap]
rs6445622	1.00[CEU][hapmap]
rs6445628	1.00[CEU][hapmap]
rs6445727	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6772668	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6774745	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6775666	0.85[CEU][hapmap]
rs6787312	1.00[CEU][hapmap]
rs7372658	0.81[EUR][1000 genomes]
rs751075	1.00[CEU][hapmap]
rs7614317	0.89[CHB][hapmap]
rs7616967	0.94[CHB][hapmap]
rs7617533	0.84[ASN][1000 genomes]
rs7623803	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7625006	1.00[CEU][hapmap]
rs7633708	0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.83[ASN][1000 genomes]
rs7640083	0.90[CHB][hapmap];0.84[CHD][hapmap];0.87[MEX][hapmap]
rs7648012	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.83[ASN][1000 genomes]
rs7649069	0.90[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap]
rs9311469	0.81[EUR][1000 genomes]
rs9832672	0.90[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap]
rs9866430	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9877188	0.90[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap]

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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7625821	HYAL2	cis	parietal	SCAN
rs7625821	TEX264	cis	Nerve Tibial	GTEx
rs7625821	IQCF2	cis	parietal	SCAN
rs7625821	MST1	cis	cerebellum	SCAN
rs7625821	TEX264	cis	Artery Tibial	GTEx
rs7625821	HEMK1	cis	cerebellum	SCAN
rs7625821	TEX264	cis	Esophagus Muscularis	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51458200-51515000	Weak transcription	Fetal Brain Male	brain
2	chr3:51467800-51524000	Weak transcription	Small Intestine	intestine
3	chr3:51477200-51515000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:51490400-51515000	Weak transcription	Stomach Mucosa	stomach
5	chr3:51491400-51532800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:51495000-51532600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:51495800-51518200	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr3:51495800-51518200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:51495800-51526800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr3:51495800-51531800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:51496000-51517800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr3:51496000-51518400	Strong transcription	Fetal Stomach	stomach
13	chr3:51496000-51531800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:51496200-51516600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:51496200-51516800	Strong transcription	Dnd41	blood
16	chr3:51496200-51518000	Strong transcription	Placenta	Placenta
17	chr3:51496200-51530600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:51496200-51531000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr3:51496400-51525800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:51497200-51524400	Weak transcription	Right Ventricle	heart
21	chr3:51497600-51518200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:51498000-51514000	Weak transcription	Brain Substantia Nigra	brain
23	chr3:51498000-51515000	Weak transcription	Esophagus	oesophagus
24	chr3:51499400-51514600	Weak transcription	NHDF-Ad	bronchial
25	chr3:51499400-51532800	Weak transcription	Fetal Heart	heart
26	chr3:51499600-51517800	Strong transcription	Fetal Intestine Small	intestine
27	chr3:51500600-51532800	Weak transcription	Fetal Kidney	kidney
28	chr3:51500800-51514800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:51501000-51514200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:51501000-51515000	Weak transcription	A549	lung
31	chr3:51501000-51532400	Weak transcription	Psoas Muscle	Psoas
32	chr3:51501000-51532800	Weak transcription	NH-A	brain
33	chr3:51503400-51514400	Weak transcription	HMEC	breast
34	chr3:51504000-51515400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:51504800-51533000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:51505000-51531600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:51505000-51533000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:51505200-51514800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:51506400-51514600	Weak transcription	NHLF	lung
40	chr3:51506400-51523200	Weak transcription	HSMMtube	muscle
41	chr3:51506600-51513800	Weak transcription	GM12878-XiMat	blood
42	chr3:51506600-51514200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:51506600-51514600	Weak transcription	Brain Angular Gyrus	brain
44	chr3:51506600-51523000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:51506600-51530800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:51506600-51532600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr3:51506600-51532600	Weak transcription	K562	blood
48	chr3:51506800-51514000	Weak transcription	Fetal Lung	lung
49	chr3:51506800-51514200	Weak transcription	Osteobl	bone
50	chr3:51506800-51514600	Weak transcription	Brain Inferior Temporal Lobe	brain

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