Variant report

Variant	rs4687800
Chromosome Location	chr3:51476387-51476388
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	chr3:51473513..51476440-chr3:51485554..51487520,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1031925	1.00[CEU][hapmap]
rs10433609	0.90[CHB][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];0.81[ASN][1000 genomes]
rs11706571	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs11917683	1.00[CEU][hapmap]
rs12632046	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[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];0.80[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1480360	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs1542574	0.88[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.95[LWK][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1552074	0.92[CEU][hapmap]
rs17051762	0.91[CEU][hapmap]
rs2127655	0.92[CEU][hapmap]
rs2164599	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2170178	0.85[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs2219890	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2219891	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs2241784	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4611808	0.83[EUR][1000 genomes]
rs4687721	1.00[CEU][hapmap]
rs4974092	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs4974094	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs4974099	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs4974104	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772668	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774745	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6787312	1.00[CEU][hapmap]
rs6796847	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs751075	1.00[CEU][hapmap]
rs7614317	0.89[CHB][hapmap]
rs7616967	0.94[CHB][hapmap]
rs7617533	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7623803	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7625006	1.00[CEU][hapmap]
rs7625821	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[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];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7640083	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
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];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7649069	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs899750	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs9832672	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs9856566	0.94[CHB][hapmap]
rs9860403	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
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
rs4687800	TEX264	cis	Artery Tibial	GTEx
rs4687800	HYAL2	cis	parietal	SCAN
rs4687800	MST1	cis	cerebellum	SCAN
rs4687800	TEX264	cis	Esophagus Muscularis	GTEx
rs4687800	TEX264	cis	Nerve Tibial	GTEx
rs4687800	IQCF2	cis	parietal	SCAN
rs4687800	HEMK1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51433400-51477400	Weak transcription	Fetal Heart	heart
2	chr3:51434200-51477600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:51435200-51478000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:51439800-51478000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:51440800-51478200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr3:51444800-51477800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:51445400-51478400	Strong transcription	Primary B cells from peripheral blood	blood
8	chr3:51451200-51476800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:51458200-51477600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:51458200-51478400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:51458200-51489400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:51458200-51515000	Weak transcription	Fetal Brain Male	brain
13	chr3:51458400-51500200	Weak transcription	Psoas Muscle	Psoas
14	chr3:51458800-51503800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:51461800-51478000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:51462400-51478200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:51462600-51477000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:51462600-51477200	Strong transcription	Placenta	Placenta
19	chr3:51462600-51477400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:51462600-51477400	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr3:51463000-51477200	Strong transcription	Liver	Liver
22	chr3:51463000-51477600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:51463200-51478000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr3:51463400-51478200	Strong transcription	Dnd41	blood
25	chr3:51463600-51477200	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:51464400-51476400	Strong transcription	Fetal Muscle Trunk	muscle
27	chr3:51467800-51482000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:51467800-51502000	Weak transcription	HMEC	breast
29	chr3:51467800-51524000	Weak transcription	Small Intestine	intestine
30	chr3:51469200-51477800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:51470600-51498400	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:51471000-51476600	Strong transcription	Fetal Stomach	stomach
33	chr3:51471600-51479000	Weak transcription	Stomach Mucosa	stomach
34	chr3:51471800-51477000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:51472000-51498000	Weak transcription	NHEK	skin
36	chr3:51472200-51477000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:51472200-51477000	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:51472200-51477200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:51472400-51476400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:51472400-51477200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:51472400-51477200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:51472400-51477200	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:51472400-51477400	Strong transcription	Adipose Nuclei	Adipose
44	chr3:51472400-51478000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr3:51472600-51476400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:51472600-51477200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:51472600-51477200	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:51472800-51476600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:51472800-51477000	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr3:51472800-51477400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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