Variant report

Variant	rs11130114
Chromosome Location	chr3:47154651-47154652
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47151756..47154654-chr3:47157875..47159694,2	K562	blood:
2	chr3:47148587..47150185-chr3:47152146..47155145,2	K562	blood:

Extended variants
information (count: 124 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10433549	0.91[CEU][hapmap]
rs10461018	1.00[CEU][hapmap]
rs1076394	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1079276	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs11130110	1.00[CEU][hapmap]
rs11130111	1.00[CEU][hapmap]
rs11130112	1.00[CEU][hapmap]
rs11130115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130123	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11130124	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs11130126	0.81[CEU][hapmap]
rs11708451	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710013	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11710322	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11712716	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11714282	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11714373	0.90[EUR][1000 genomes]
rs11716539	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11718795	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11719306	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11719738	0.91[EUR][1000 genomes]
rs11720139	0.92[CEU][hapmap]
rs11915074	0.82[CEU][hapmap]
rs11920853	0.82[CEU][hapmap]
rs11923706	0.85[EUR][1000 genomes]
rs12488225	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12489211	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12493425	0.91[EUR][1000 genomes]
rs12629262	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12635619	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13061071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13062022	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13063250	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13078131	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13084117	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13091054	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13094438	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs13094672	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098228	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1466740	0.83[EUR][1000 genomes]
rs1466741	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1638676	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs17784127	0.88[CEU][hapmap]
rs1811652	0.91[EUR][1000 genomes]
rs2061197	1.00[CEU][hapmap]
rs2132173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276853	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs2276854	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[ASN][1000 genomes]
rs2278963	0.92[CEU][hapmap]
rs2290546	0.82[JPT][hapmap]
rs2305634	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2305635	0.92[CEU][hapmap]
rs2305638	0.92[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs2385867	0.81[ASN][1000 genomes]
rs295441	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs295442	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs34103310	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4018905	0.88[EUR][1000 genomes]
rs4078466	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4082155	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4234465	1.00[CEU][hapmap]
rs4587	0.82[JPT][hapmap]
rs4682837	1.00[CEU][hapmap]
rs4682844	1.00[CEU][hapmap]
rs4682852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683297	0.81[JPT][hapmap]
rs4683298	0.81[JPT][hapmap]
rs4683320	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683322	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs4683324	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4683326	0.88[CEU][hapmap];0.96[YRI][hapmap]
rs57756484	0.86[EUR][1000 genomes]
rs58956475	0.90[EUR][1000 genomes]
rs62246451	0.91[EUR][1000 genomes]
rs62246455	0.87[EUR][1000 genomes]
rs6414435	0.81[EUR][1000 genomes]
rs6414436	0.85[EUR][1000 genomes]
rs6442040	0.81[JPT][hapmap]
rs6442055	0.80[EUR][1000 genomes]
rs6442059	0.91[EUR][1000 genomes]
rs6763236	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6766230	0.91[EUR][1000 genomes]
rs6767907	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs6768221	0.81[CEU][hapmap]
rs6772670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6773521	0.87[EUR][1000 genomes]
rs6777145	0.80[EUR][1000 genomes]
rs6781941	0.85[EUR][1000 genomes]
rs6785790	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791062	0.89[EUR][1000 genomes]
rs6791842	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs6794193	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7433300	0.83[CEU][hapmap]
rs749511	0.92[CEU][hapmap]
rs749512	0.88[CEU][hapmap]
rs7610636	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7615323	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7620997	0.81[EUR][1000 genomes]
rs7621911	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7623888	0.80[EUR][1000 genomes]
rs7625067	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7625070	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7628747	1.00[CEU][hapmap]
rs7637302	0.80[ASN][1000 genomes]
rs7645278	0.81[JPT][hapmap]
rs807932	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs807936	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs811115	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs9311403	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs9812878	0.81[EUR][1000 genomes]
rs9818382	0.91[EUR][1000 genomes]
rs9821119	0.91[EUR][1000 genomes]
rs9837343	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs9843075	0.87[EUR][1000 genomes]
rs9852082	0.81[JPT][hapmap]
rs9854790	0.80[EUR][1000 genomes]
rs9855938	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	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
5	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1002970	chr3:47120592-47170607	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv590210	chr3:47126543-47214122	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11130114	RTP3	cis	lesional skin	skin_eQTL
rs11130114	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs11130114	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47123000-47159200	Weak transcription	Brain Substantia Nigra	brain
2	chr3:47125800-47155000	Strong transcription	Primary B cells from peripheral blood	blood
3	chr3:47126400-47159800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr3:47126800-47168200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:47135000-47158800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:47139600-47161800	Weak transcription	Fetal Brain Female	brain
7	chr3:47139800-47163200	Weak transcription	A549	lung
8	chr3:47140000-47175600	Weak transcription	Small Intestine	intestine
9	chr3:47140600-47159200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:47141200-47155000	Weak transcription	HMEC	breast
11	chr3:47141200-47155200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:47144200-47155000	Weak transcription	Right Ventricle	heart
13	chr3:47144200-47170800	Weak transcription	Brain Angular Gyrus	brain
14	chr3:47145000-47155000	Strong transcription	GM12878-XiMat	blood
15	chr3:47145200-47154800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr3:47145600-47155800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:47145800-47175000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:47146400-47164600	Weak transcription	Psoas Muscle	Psoas
19	chr3:47149000-47157600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:47149200-47157600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:47149200-47159000	Strong transcription	Fetal Thymus	thymus
22	chr3:47149600-47160000	Strong transcription	Liver	Liver
23	chr3:47149800-47155600	Strong transcription	Thymus	Thymus
24	chr3:47149800-47156800	Strong transcription	K562	blood
25	chr3:47149800-47159600	Strong transcription	Dnd41	blood
26	chr3:47150000-47158400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:47150000-47158800	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:47150200-47158600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:47150200-47158600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:47150200-47158800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr3:47150400-47158600	Strong transcription	Primary hematopoietic stem cells	blood
32	chr3:47150400-47158800	Strong transcription	Adipose Nuclei	Adipose
33	chr3:47150600-47155000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr3:47150600-47160600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:47150800-47156600	Strong transcription	Fetal Intestine Small	intestine
36	chr3:47150800-47156600	Strong transcription	Fetal Stomach	stomach
37	chr3:47150800-47157400	Strong transcription	Primary T cells from cord blood	blood
38	chr3:47150800-47158600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:47150800-47161000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:47150800-47161400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr3:47150800-47166600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr3:47151200-47164400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr3:47151200-47164400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:47151200-47167400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:47151400-47159600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr3:47151400-47161600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:47151600-47155000	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:47151600-47155400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:47151600-47157200	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr3:47151600-47158400	Strong transcription	Hela-S3	cervix

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