Variant report

Variant	rs11130128
Chromosome Location	chr3:47486632-47486633
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1038394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1076394	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs10865946	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130124	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs11130126	0.88[CEU][hapmap]
rs11130127	0.86[AMR][1000 genomes]
rs11130129	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130132	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130133	0.88[EUR][1000 genomes]
rs11130137	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11705957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11707895	0.85[EUR][1000 genomes]
rs11710013	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs11710121	0.88[CEU][hapmap]
rs11710322	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs11711265	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11711824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11712445	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11713413	0.83[EUR][1000 genomes]
rs11716763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11719877	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11914913	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11914932	0.88[EUR][1000 genomes]
rs11915074	0.89[CEU][hapmap]
rs11920853	0.89[CEU][hapmap]
rs11925823	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11927371	0.83[AMR][1000 genomes]
rs12486969	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12487736	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12489046	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12490058	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12490383	0.84[ASN][1000 genomes]
rs12492433	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12495169	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs12497225	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12630641	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12632132	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12636851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13059519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13064843	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13075233	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13079098	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1531875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1638676	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs17080872	0.83[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs17410853	0.88[CEU][hapmap]
rs17411375	0.96[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes]
rs17784882	1.00[CEU][hapmap];0.90[YRI][hapmap];0.90[EUR][1000 genomes]
rs1872164	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1872166	0.90[YRI][hapmap]
rs2062278	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2101247	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2159400	0.96[CEU][hapmap];0.83[AMR][1000 genomes]
rs2291298	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs295428	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs295441	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs295442	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs295449	0.96[CEU][hapmap]
rs295458	0.96[CEU][hapmap];0.80[JPT][hapmap]
rs295461	0.96[CEU][hapmap]
rs34634681	0.84[EUR][1000 genomes]
rs3736177	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3816779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4241548	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4599332	0.84[EUR][1000 genomes]
rs4683326	0.96[CEU][hapmap]
rs4858805	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4858811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4858824	1.00[CEU][hapmap]
rs4858848	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858856	0.86[EUR][1000 genomes]
rs4858868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4858888	0.90[AMR][1000 genomes]
rs4858890	0.89[AMR][1000 genomes]
rs4858893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4858894	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56032309	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56351005	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57346147	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59586735	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60369822	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246474	0.86[AMR][1000 genomes]
rs62248599	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62248603	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62248605	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62260710	0.87[EUR][1000 genomes]
rs62260711	0.87[EUR][1000 genomes]
rs62260741	0.82[EUR][1000 genomes]
rs6765990	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6768221	0.89[CEU][hapmap]
rs6780013	0.92[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs6787422	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6790763	0.83[EUR][1000 genomes]
rs6792461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6792488	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6800271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73081205	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7613282	0.87[AMR][1000 genomes]
rs7628631	0.88[EUR][1000 genomes]
rs7641010	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7649234	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7651194	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs807932	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs807936	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs811115	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs8180040	0.87[AMR][1000 genomes]
rs878659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs922957	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9683033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9683177	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv511233	chr3:47484797-47494157	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv590212	chr3:47485029-47500662	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11130128	RTP3	cis	lesional skin	skin_eQTL
rs11130128	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs11130128	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47473200-47487200	Weak transcription	HUVEC	blood vessel
2	chr3:47474600-47489600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:47476600-47514200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:47481400-47496000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:47481400-47500600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:47481800-47492600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:47482200-47488800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:47483200-47487400	Enhancers	Liver	Liver
9	chr3:47484000-47507800	Weak transcription	Primary B cells from cord blood	blood
10	chr3:47484000-47511200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:47484200-47511200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr3:47484400-47492600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:47484400-47497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr3:47484600-47486800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:47484600-47487400	Weak transcription	Fetal Brain Female	brain
16	chr3:47484600-47490000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:47484600-47494200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:47484600-47497400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:47484600-47500600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:47484600-47514000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:47484600-47514200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:47484600-47514200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:47484600-47514200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:47484600-47514800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:47484800-47487000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr3:47484800-47487400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:47484800-47504400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:47484800-47504600	Weak transcription	Primary T cells from cord blood	blood
29	chr3:47484800-47514800	Weak transcription	Thymus	Thymus
30	chr3:47485000-47487400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:47485000-47487400	Weak transcription	Dnd41	blood
32	chr3:47485000-47514800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:47485200-47502600	Weak transcription	K562	blood
34	chr3:47485400-47488600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:47485400-47489400	Weak transcription	GM12878-XiMat	blood
36	chr3:47485400-47490800	Weak transcription	Fetal Lung	lung
37	chr3:47485400-47493000	Weak transcription	Spleen	Spleen
38	chr3:47485400-47494200	Weak transcription	Ovary	ovary
39	chr3:47485400-47503200	Weak transcription	Gastric	stomach
40	chr3:47485600-47493200	Weak transcription	Esophagus	oesophagus
41	chr3:47485600-47494000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr3:47485800-47493600	Weak transcription	Fetal Heart	heart
43	chr3:47486000-47488600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:47486000-47490800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:47486000-47492200	Weak transcription	Psoas Muscle	Psoas
46	chr3:47486000-47494200	Weak transcription	Left Ventricle	heart
47	chr3:47486000-47497200	Weak transcription	A549	lung
48	chr3:47486000-47497400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:47486000-47500200	Weak transcription	Fetal Intestine Large	intestine
50	chr3:47486000-47500400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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