Variant report

Variant	rs295458
Chromosome Location	chr3:47385585-47385586
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47383805..47386374-chr3:47389680..47393149,3	K562	blood:
2	chr3:47378756..47381001-chr3:47384460..47386861,2	K562	blood:
3	chr3:47384263..47385776-chr3:47386052..47388826,2	K562	blood:
4	chr3:47384276..47387136-chr3:47387326..47388851,2	K562	blood:
5	chr3:47376336..47377956-chr3:47383813..47385587,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1038394	0.92[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1076394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs10865946	0.96[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130123	0.85[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap]
rs11130124	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs11130126	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs11130127	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130128	0.96[CEU][hapmap];0.80[JPT][hapmap]
rs11130129	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs11130137	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs11705957	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs11710013	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap]
rs11710121	0.85[CEU][hapmap]
rs11710322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs11711265	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap]
rs11711824	0.92[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];0.83[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11712445	0.96[CEU][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11716763	0.96[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs11719877	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11915074	0.92[CEU][hapmap]
rs11920853	0.92[CEU][hapmap]
rs11925823	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11927371	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12486969	0.86[EUR][1000 genomes]
rs12487736	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12495169	0.84[JPT][hapmap]
rs12497225	0.87[EUR][1000 genomes]
rs12632132	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12636851	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs13059519	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs13064843	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13072802	0.86[AFR][1000 genomes]
rs13075233	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13079098	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13094438	0.85[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap]
rs1531875	0.92[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1564760	0.85[YRI][hapmap]
rs1638676	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs17080872	0.81[JPT][hapmap]
rs17410853	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs17411375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17784882	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs1872164	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs2062278	0.87[EUR][1000 genomes]
rs2101247	0.92[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs2132173	0.85[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs2159400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276853	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap]
rs2276854	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs2291298	0.96[CEU][hapmap];0.94[YRI][hapmap]
rs295428	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295433	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs295441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs295442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs295449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295461	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3736177	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs3816779	0.85[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.84[LWK][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs4241548	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4683326	1.00[CEU][hapmap]
rs4858805	0.86[EUR][1000 genomes]
rs4858811	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs4858824	0.96[CEU][hapmap]
rs4858848	0.85[EUR][1000 genomes]
rs4858868	0.92[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4858888	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858890	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858893	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs4858894	0.87[CEU][hapmap];0.88[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes]
rs553989	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56032309	0.87[EUR][1000 genomes]
rs56351005	0.86[EUR][1000 genomes]
rs57346147	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60369822	0.81[EUR][1000 genomes]
rs62246474	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6768221	0.92[CEU][hapmap]
rs6772670	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs6780013	0.89[CEU][hapmap];0.86[TSI][hapmap]
rs6787422	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6791842	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap]
rs6792461	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs6800271	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7613282	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641010	0.83[EUR][1000 genomes]
rs7651762	0.96[CEU][hapmap];0.80[JPT][hapmap];0.86[EUR][1000 genomes]
rs807810	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs807931	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs807932	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs807936	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs811115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs8180040	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs878659	0.92[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.99[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs922957	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs9683033	0.92[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.99[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes]
rs9683177	0.87[AMR][1000 genomes]

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	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs295458	SCAP	cis	parietal	SCAN
rs295458	PRKAR2A	cis	cerebellum	SCAN
rs295458	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs295458	HYAL2	cis	cerebellum	SCAN
rs295458	AMIGO3	cis	cerebellum	SCAN
rs295458	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs295458	C3orf75	cis	cerebellum	SCAN
rs295458	RTP3	cis	lesional skin	skin_eQTL
rs295458	CCDC12	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47358800-47387000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr3:47359400-47387200	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr3:47359400-47387800	Strong transcription	Spleen	Spleen
4	chr3:47359600-47386800	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr3:47360000-47388200	Strong transcription	Fetal Intestine Large	intestine
6	chr3:47360400-47387000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:47360400-47388000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:47360600-47387000	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr3:47360600-47387200	Strong transcription	Primary B cells from peripheral blood	blood
10	chr3:47360600-47387600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:47360600-47387600	Strong transcription	Fetal Thymus	thymus
12	chr3:47360600-47387800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:47360600-47387800	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:47360600-47388200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr3:47360600-47388800	Strong transcription	Primary T cells from cord blood	blood
16	chr3:47360800-47386800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:47360800-47388000	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:47361000-47387400	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr3:47361000-47387800	Strong transcription	Brain Cingulate Gyrus	brain
20	chr3:47361000-47388000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:47361000-47388200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:47361000-47388200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr3:47361200-47387600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:47361200-47388000	Strong transcription	Adipose Nuclei	Adipose
25	chr3:47361200-47388000	Strong transcription	Stomach Smooth Muscle	stomach
26	chr3:47361400-47388000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr3:47361400-47389800	Weak transcription	Right Atrium	heart
28	chr3:47361800-47386600	Strong transcription	Lung	lung
29	chr3:47361800-47387400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:47361800-47388200	Strong transcription	Fetal Brain Female	brain
31	chr3:47362200-47388600	Strong transcription	Brain Germinal Matrix	brain
32	chr3:47363800-47387400	Weak transcription	Stomach Mucosa	stomach
33	chr3:47365600-47387600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:47365600-47388000	Strong transcription	Placenta	Placenta
35	chr3:47365600-47388200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:47365600-47388200	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:47365600-47388200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:47365800-47387600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:47366200-47388800	Strong transcription	Fetal Stomach	stomach
40	chr3:47366800-47387400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:47367600-47387800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:47367800-47387000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr3:47367800-47387000	Strong transcription	GM12878-XiMat	blood
44	chr3:47367800-47387000	Strong transcription	K562	blood
45	chr3:47367800-47387400	Strong transcription	Primary B cells from cord blood	blood
46	chr3:47367800-47388000	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:47368200-47386400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:47368600-47386200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:47368800-47386600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:47369200-47387600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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