Variant report

Variant	rs10790
Chromosome Location	chr3:142778666-142778667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142771385..142780409-chr3:142780501..142789449,10	K562	blood:
2	chr3:142773649..142775353-chr3:142777692..142779387,2	K562	blood:
3	chr3:142777135..142778996-chr3:142838578..142841035,2	K562	blood:

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10413	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1043898	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451867	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10513184	0.85[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1053950	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935475	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10935479	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709036	0.85[CEU][hapmap];0.80[CHB][hapmap];0.80[TSI][hapmap]
rs11915462	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11922201	0.84[EUR][1000 genomes]
rs12485790	0.81[EUR][1000 genomes]
rs12490776	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12492904	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12695770	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13075955	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13088422	0.83[EUR][1000 genomes]
rs13094293	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13099995	0.84[EUR][1000 genomes]
rs1349262	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13715	0.85[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1375814	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1449868	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1449869	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1530753	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1532588	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1545597	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17557029	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1814565	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs1827159	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1839406	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1868569	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868570	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965343	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2045306	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124541	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2124542	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2124543	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2137586	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[EUR][1000 genomes]
rs2175739	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[EUR][1000 genomes]
rs2290549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2353408	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2353409	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2353411	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs251490	0.82[CEU][hapmap]
rs251491	0.82[CEU][hapmap]
rs36285	0.82[CEU][hapmap]
rs3821645	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3856697	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3902877	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4030582	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683444	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683721	0.87[EUR][1000 genomes]
rs4683722	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683723	0.88[EUR][1000 genomes]
rs4683724	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56382522	0.85[EUR][1000 genomes]
rs6440129	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440131	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440132	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440133	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440134	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770102	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6778454	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6781080	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6781887	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6783145	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6784200	0.89[CEU][hapmap];0.90[CHB][hapmap];0.82[TSI][hapmap]
rs6796771	0.83[EUR][1000 genomes]
rs6805417	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6806551	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6808689	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7611721	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7623532	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644475	0.81[EUR][1000 genomes]
rs7648143	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7649225	0.87[EUR][1000 genomes]
rs7652745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs766360	0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs936194	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs936196	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs936197	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs937498	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9814656	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816317	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9835348	0.89[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9847059	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851353	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862433	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877128	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9877135	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv591921	chr3:142762487-142841740	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1004467	chr3:142768867-142800605	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1004682	chr3:142768867-142804154	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10790	U2SURP	cis	lymphoblastoid	seeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142729200-142785200	Weak transcription	Aorta	Aorta
2	chr3:142734400-142785200	Weak transcription	Esophagus	oesophagus
3	chr3:142749000-142784200	Weak transcription	Small Intestine	intestine
4	chr3:142749200-142779000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:142763400-142787000	Weak transcription	Spleen	Spleen
6	chr3:142764200-142784200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:142764800-142779600	Weak transcription	Fetal Brain Male	brain
8	chr3:142765000-142782200	Weak transcription	Fetal Heart	heart
9	chr3:142765400-142791600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:142766800-142778800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:142766800-142778800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:142766800-142779000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:142766800-142779000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:142766800-142780800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:142766800-142780800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:142766800-142781000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:142766800-142781600	Strong transcription	Dnd41	blood
18	chr3:142767400-142781400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:142767400-142786600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:142769200-142782800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:142769600-142789000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:142770400-142787000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:142770600-142779000	Strong transcription	Primary B cells from cord blood	blood
24	chr3:142771200-142781800	Weak transcription	Lung	lung
25	chr3:142771200-142790000	Weak transcription	Pancreas	Pancrea
26	chr3:142771400-142786600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:142771600-142780400	Weak transcription	Right Ventricle	heart
28	chr3:142771600-142786600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:142772200-142784800	Weak transcription	Fetal Stomach	stomach
30	chr3:142773000-142783200	Weak transcription	Fetal Intestine Small	intestine
31	chr3:142773000-142783400	Weak transcription	Colonic Mucosa	Colon
32	chr3:142773000-142783400	Weak transcription	Left Ventricle	heart
33	chr3:142773000-142783400	Weak transcription	Thymus	Thymus
34	chr3:142773000-142790200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:142773400-142785200	Weak transcription	Fetal Kidney	kidney
36	chr3:142773400-142788800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:142774000-142778800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:142774000-142780200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:142774000-142780400	Weak transcription	Brain Germinal Matrix	brain
40	chr3:142774000-142781800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:142774000-142785200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:142774000-142785800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:142774200-142782000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:142774200-142784200	Weak transcription	Ovary	ovary
45	chr3:142774200-142789400	Weak transcription	NHLF	lung
46	chr3:142774400-142785200	Weak transcription	Fetal Brain Female	brain
47	chr3:142775000-142779000	Weak transcription	Psoas Muscle	Psoas
48	chr3:142775000-142786400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:142775200-142781800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:142775200-142789200	Weak transcription	NHDF-Ad	bronchial

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