Variant report

Variant	rs1872164
Chromosome Location	chr3:47415100-47415101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47411630..47415396-chr3:47420352..47423436,6	K562	blood:
2	chr3:46924051..46925925-chr3:47412660..47415273,2	K562	blood:
3	chr3:47414574..47416766-chr3:47420755..47422470,2	MCF-7	breast:
4	chr3:47409105..47415396-chr3:47419096..47424075,13	K562	blood:

Variant related genes	Relation type
ENSG00000260236	Chromatin interaction
ENSG00000160801	Chromatin interaction
ENSG00000076201	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1038394	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1076394	0.96[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs10865946	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]
rs11130123	0.92[CEU][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs11130124	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs11130126	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs11130127	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11130128	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]
rs11130129	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130132	0.83[EUR][1000 genomes]
rs11130133	0.81[EUR][1000 genomes]
rs11130137	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs11705957	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11710013	0.96[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs11710121	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs11710322	0.96[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs11711265	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs11711824	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11712445	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11716763	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs11719877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11914913	0.81[EUR][1000 genomes]
rs11914932	0.81[EUR][1000 genomes]
rs11915074	0.88[CEU][hapmap]
rs11920853	0.88[CEU][hapmap]
rs11925823	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11927371	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12486969	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487736	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12489046	0.86[EUR][1000 genomes]
rs12490058	0.83[EUR][1000 genomes]
rs12492433	0.86[EUR][1000 genomes]
rs12495169	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs12497225	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12630641	0.81[EUR][1000 genomes]
rs12632132	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12636851	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13059519	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs13064843	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13079098	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13094438	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs1531875	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1564760	0.81[GIH][hapmap]
rs1638676	0.96[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs17080872	0.87[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs17410853	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs17411375	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17784882	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs1872166	0.91[YRI][hapmap]
rs2062278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2101247	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2132173	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs2159400	0.96[CEU][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2276853	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs2276854	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs2291298	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs295428	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs295441	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs295442	0.96[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs295449	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs295458	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs295461	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs3736177	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816779	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4241548	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4683326	0.96[CEU][hapmap]
rs4858805	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858811	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4858824	1.00[CEU][hapmap]
rs4858848	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4858868	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858888	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4858890	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4858893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4858894	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs553989	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56032309	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56351005	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57346147	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59586735	0.86[EUR][1000 genomes]
rs60369822	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62246474	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62248580	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62248599	0.85[EUR][1000 genomes]
rs6765990	0.82[EUR][1000 genomes]
rs6768221	0.88[CEU][hapmap]
rs6780013	0.86[ASW][hapmap];0.92[CEU][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6787422	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791842	0.96[CEU][hapmap]
rs6792461	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6792488	0.87[EUR][1000 genomes]
rs6800271	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73081205	0.84[EUR][1000 genomes]
rs7613282	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7628631	0.81[EUR][1000 genomes]
rs7641010	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7649234	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7651194	0.82[EUR][1000 genomes]
rs7651762	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs807810	0.89[EUR][1000 genomes]
rs807931	0.87[EUR][1000 genomes]
rs807932	0.92[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs807936	0.96[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs811115	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs8180040	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs878659	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs922957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9683033	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9683177	0.87[EUR][1000 genomes];0.81[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1872164	CCDC12	cis	cerebellum	SCAN
rs1872164	C3orf75	cis	cerebellum	SCAN
rs1872164	RTP3	cis	lesional skin	skin_eQTL
rs1872164	HYAL2	cis	cerebellum	SCAN
rs1872164	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs1872164	SMARCC1	cis	lymphoblastoid	seeQTL
rs1872164	IFRD2	cis	parietal	SCAN
rs1872164	PRKAR2A	cis	cerebellum	SCAN
rs1872164	AMIGO3	cis	cerebellum	SCAN
rs1872164	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs1872164	SCAP	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47401600-47421200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:47412600-47415200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr3:47412800-47417800	Weak transcription	HepG2	liver
4	chr3:47413200-47418000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:47413200-47418000	Weak transcription	K562	blood
6	chr3:47413200-47418400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:47413200-47418600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:47413200-47418800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:47413200-47418800	Weak transcription	Liver	Liver
10	chr3:47413200-47420200	Weak transcription	Spleen	Spleen
11	chr3:47413200-47420400	Weak transcription	Fetal Intestine Large	intestine
12	chr3:47413200-47420600	Weak transcription	Adipose Nuclei	Adipose
13	chr3:47413400-47420400	Weak transcription	Fetal Intestine Small	intestine
14	chr3:47413400-47420800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:47413600-47421000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:47414000-47418200	Weak transcription	Fetal Stomach	stomach
17	chr3:47414200-47418400	Weak transcription	Primary B cells from cord blood	blood
18	chr3:47414200-47421000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:47414800-47418200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr3:47415000-47418000	Weak transcription	Primary monocytes fromperipheralblood	blood

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