Variant report

Variant	rs10865946
Chromosome Location	chr3:47425060-47425061
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:47424960-47425134	K562	blood:	n/a	n/a
2	GATA3	chr3:47425002-47425350	T-47D	breast:	n/a	chr3:47425301-47425308

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47423869..47425978-chr3:47441656..47444550,3	K562	blood:

Variant related genes	Relation type
ENSG00000260236	TF binding region

Extended variants
information (count: 112 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1038394	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1076394	0.96[CEU][hapmap]
rs11130123	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs11130124	0.96[CEU][hapmap]
rs11130126	0.88[CEU][hapmap]
rs11130127	0.88[EUR][1000 genomes]
rs11130128	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130129	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130132	0.82[EUR][1000 genomes]
rs11130137	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11705957	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11710013	0.96[CEU][hapmap]
rs11710121	0.88[CEU][hapmap]
rs11710322	0.96[CEU][hapmap]
rs11711265	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs11711824	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11712445	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11716763	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs11719877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11914932	0.80[EUR][1000 genomes]
rs11915074	0.89[CEU][hapmap]
rs11920853	0.89[CEU][hapmap]
rs11925823	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11927371	0.84[EUR][1000 genomes]
rs12486969	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12487736	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12489046	0.86[EUR][1000 genomes]
rs12490058	0.82[EUR][1000 genomes]
rs12490383	0.81[CHB][hapmap]
rs12492433	0.86[EUR][1000 genomes]
rs12495169	0.87[CHB][hapmap]
rs12497225	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12630641	0.80[EUR][1000 genomes]
rs12632132	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12636851	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13059519	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs13064843	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13075233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079098	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13094438	0.96[CEU][hapmap]
rs1531875	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1564760	0.90[YRI][hapmap]
rs1638676	0.96[CEU][hapmap];0.89[YRI][hapmap]
rs17080872	0.87[CHB][hapmap]
rs17410853	0.88[CEU][hapmap]
rs17411375	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs17784882	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1872164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2062278	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2101247	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2132173	0.85[CEU][hapmap]
rs2159400	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2276853	0.96[CEU][hapmap]
rs2276854	0.96[CEU][hapmap]
rs2291298	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs295428	0.96[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs295433	0.94[YRI][hapmap]
rs295441	0.96[CEU][hapmap];0.90[YRI][hapmap]
rs295442	0.96[CEU][hapmap]
rs295449	0.96[CEU][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs295458	0.96[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs295461	0.96[CEU][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3736177	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3816779	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs4241548	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4683326	0.96[CEU][hapmap]
rs4858805	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858811	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs4858824	1.00[CEU][hapmap]
rs4858848	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858868	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858888	0.88[EUR][1000 genomes]
rs4858890	0.82[EUR][1000 genomes]
rs4858893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4858894	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs553989	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56032309	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56351005	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57346147	0.99[EUR][1000 genomes]
rs59586735	0.85[EUR][1000 genomes]
rs60369822	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62246474	0.88[EUR][1000 genomes]
rs62248580	0.90[EUR][1000 genomes]
rs62248599	0.84[EUR][1000 genomes]
rs6765990	0.81[EUR][1000 genomes]
rs6768221	0.88[CEU][hapmap]
rs6780013	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs6787422	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6791842	0.96[CEU][hapmap]
rs6792461	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6792488	0.86[EUR][1000 genomes]
rs6800271	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73081205	0.83[EUR][1000 genomes]
rs7613282	0.87[EUR][1000 genomes]
rs7628631	0.80[EUR][1000 genomes]
rs7641010	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7649234	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7651194	0.81[EUR][1000 genomes]
rs7651762	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs807810	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs807931	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs807932	0.92[CEU][hapmap];0.94[YRI][hapmap]
rs807936	0.96[CEU][hapmap];0.89[YRI][hapmap]
rs811115	0.95[CEU][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap]
rs8180040	0.86[EUR][1000 genomes]
rs878659	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs922957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9683033	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9683177	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[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	esv1807553	chr3:47393616-47470763	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv3802	chr3:47396674-47441951	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10865946	RTP3	cis	lesional skin	skin_eQTL
rs10865946	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs10865946	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47423600-47425200	Weak transcription	Left Ventricle	heart
2	chr3:47423600-47425400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr3:47423600-47425400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr3:47423600-47425400	Enhancers	Pancreas	Pancrea
5	chr3:47423600-47425600	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr3:47423600-47426400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:47423600-47427000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:47423600-47427000	Weak transcription	Esophagus	oesophagus
9	chr3:47423600-47427200	Weak transcription	Right Ventricle	heart
10	chr3:47423600-47429400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:47423600-47431800	Weak transcription	Lung	lung
12	chr3:47423600-47435400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:47423600-47435400	Weak transcription	Aorta	Aorta
14	chr3:47423600-47446000	Weak transcription	Colonic Mucosa	Colon
15	chr3:47423800-47425200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:47423800-47425200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:47423800-47425200	Weak transcription	Fetal Stomach	stomach
18	chr3:47423800-47425400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:47423800-47425400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:47423800-47425400	Enhancers	Adipose Nuclei	Adipose
21	chr3:47423800-47425400	Enhancers	Brain Germinal Matrix	brain
22	chr3:47423800-47425400	Enhancers	Duodenum Mucosa	Duodenum
23	chr3:47423800-47425600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:47423800-47425600	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr3:47423800-47425600	Enhancers	Fetal Intestine Large	intestine
26	chr3:47423800-47425600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr3:47423800-47425800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:47423800-47426000	Weak transcription	HMEC	breast
29	chr3:47423800-47426600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr3:47423800-47426600	Weak transcription	Osteobl	bone
31	chr3:47423800-47426800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:47423800-47426800	Weak transcription	Stomach Mucosa	stomach
33	chr3:47423800-47426800	Weak transcription	Thymus	Thymus
34	chr3:47423800-47427000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:47423800-47427200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:47423800-47427400	Weak transcription	HSMM	muscle
37	chr3:47423800-47429400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:47423800-47429800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:47423800-47429800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:47423800-47429800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:47423800-47430200	Weak transcription	HUVEC	blood vessel
42	chr3:47423800-47430400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr3:47423800-47433800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:47423800-47435000	Weak transcription	Fetal Heart	heart
45	chr3:47423800-47435000	Weak transcription	NHDF-Ad	bronchial
46	chr3:47423800-47435400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:47423800-47435400	Weak transcription	Fetal Lung	lung
48	chr3:47423800-47435400	Weak transcription	NH-A	brain
49	chr3:47423800-47435600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:47423800-47435600	Weak transcription	Rectal Smooth Muscle	rectum

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