Variant report

Variant	rs2164599
Chromosome Location	chr3:51515229-51515230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs11130290	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs11130293	0.82[EUR][1000 genomes]
rs11706571	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs11709482	0.81[AMR][1000 genomes]
rs11719995	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11721253	0.82[EUR][1000 genomes]
rs11917683	1.00[CEU][hapmap]
rs12632046	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1318649	0.90[CHB][hapmap];0.88[CHD][hapmap];0.87[MEX][hapmap]
rs1383251	1.00[CEU][hapmap]
rs1480353	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[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];0.83[EUR][1000 genomes];0.84[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];0.81[EUR][1000 genomes]
rs1552074	0.92[CEU][hapmap]
rs17051762	0.91[CEU][hapmap]
rs2127655	0.92[CEU][hapmap]
rs2219890	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[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];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2219891	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs2241784	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[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	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974104	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[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];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4974105	1.00[CEU][hapmap]
rs4974108	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs6445601	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs6445604	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs6445611	0.90[CHB][hapmap];0.88[CHD][hapmap];0.87[MEX][hapmap]
rs6445620	1.00[CEU][hapmap]
rs6445622	1.00[CEU][hapmap]
rs6445628	1.00[CEU][hapmap]
rs6445727	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6772668	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6774745	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6775666	0.85[CEU][hapmap]
rs6787312	1.00[CEU][hapmap]
rs7372658	0.82[EUR][1000 genomes]
rs751075	1.00[CEU][hapmap]
rs7614317	0.89[CHB][hapmap]
rs7616967	0.94[CHB][hapmap]
rs7617533	0.83[ASN][1000 genomes]
rs7623803	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7625006	1.00[CEU][hapmap]
rs7625821	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7633708	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[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];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs7648012	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs7649069	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs9311469	0.82[EUR][1000 genomes]
rs9832672	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs9866430	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9877188	0.90[CHB][hapmap];0.86[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
rs2164599	HYAL2	cis	parietal	SCAN
rs2164599	TEX264	cis	Artery Tibial	GTEx
rs2164599	MST1	cis	cerebellum	SCAN
rs2164599	TEX264	cis	Nerve Tibial	GTEx
rs2164599	TEX264	cis	Esophagus Muscularis	GTEx
rs2164599	IQCF2	cis	parietal	SCAN
rs2164599	HEMK1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51467800-51524000	Weak transcription	Small Intestine	intestine
2	chr3:51491400-51532800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:51495000-51532600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:51495800-51518200	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr3:51495800-51518200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:51495800-51526800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:51495800-51531800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:51496000-51517800	Strong transcription	Fetal Muscle Trunk	muscle
9	chr3:51496000-51518400	Strong transcription	Fetal Stomach	stomach
10	chr3:51496000-51531800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:51496200-51516600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:51496200-51516800	Strong transcription	Dnd41	blood
13	chr3:51496200-51518000	Strong transcription	Placenta	Placenta
14	chr3:51496200-51530600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:51496200-51531000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:51496400-51525800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:51497200-51524400	Weak transcription	Right Ventricle	heart
18	chr3:51497600-51518200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr3:51499400-51532800	Weak transcription	Fetal Heart	heart
20	chr3:51499600-51517800	Strong transcription	Fetal Intestine Small	intestine
21	chr3:51500600-51532800	Weak transcription	Fetal Kidney	kidney
22	chr3:51501000-51532400	Weak transcription	Psoas Muscle	Psoas
23	chr3:51501000-51532800	Weak transcription	NH-A	brain
24	chr3:51504000-51515400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:51504800-51533000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:51505000-51531600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:51505000-51533000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:51506400-51523200	Weak transcription	HSMMtube	muscle
29	chr3:51506600-51523000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:51506600-51530800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:51506600-51532600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:51506600-51532600	Weak transcription	K562	blood
33	chr3:51507400-51516800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:51507600-51515600	Strong transcription	Primary T cells from cord blood	blood
35	chr3:51507800-51516800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:51508200-51529800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:51508600-51518000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:51509000-51526400	Strong transcription	Fetal Thymus	thymus
39	chr3:51509600-51518200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:51509800-51525200	Weak transcription	Colonic Mucosa	Colon
41	chr3:51510200-51520400	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr3:51510600-51522000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr3:51511000-51515400	Strong transcription	Primary hematopoietic stem cells	blood
44	chr3:51511000-51518200	Strong transcription	Liver	Liver
45	chr3:51511200-51516600	Strong transcription	Stomach Smooth Muscle	stomach
46	chr3:51511200-51519800	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:51511400-51518000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:51511400-51519600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:51511400-51526600	Strong transcription	Duodenum Mucosa	Duodenum
50	chr3:51511600-51516400	Strong transcription	Brain Germinal Matrix	brain

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