Variant report

Variant	rs1076394
Chromosome Location	chr3:47322781-47322782
allele	A/G
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	chr3:47321384-47325284	MCF10A-Er-Src	breast:	n/a	n/a
2	EBF1	chr3:47322628-47322798	GM12878	blood:	n/a	chr3:47322693-47322706 chr3:47322693-47322704
3	POLR2A	chr3:47321796-47324876	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:47322573-47322815	HepG2	liver:	n/a	n/a
5	EBF1	chr3:47322531-47322883	GM12878	blood:	n/a	chr3:47322693-47322706 chr3:47322693-47322704
6	EBF1	chr3:47322553-47322808	GM12878	blood:	n/a	chr3:47322693-47322706 chr3:47322693-47322704
7	POLR2A	chr3:47322145-47323720	A549	lung:	n/a	n/a
8	POLR2A	chr3:47322096-47324639	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:47322067-47324681	IMR90	lung:	n/a	n/a
10	HEY1	chr3:47322572-47322931	K562	blood:	n/a	n/a
11	RPC155	chr3:47322604-47323318	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr3:47322515-47325911	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr3:47321218-47324899	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47306715..47308916-chr3:47322571..47324674,2	MCF-7	breast:
2	chr3:47321814..47325452-chr3:47418885..47424380,8	K562	blood:
3	chr3:47318429..47320664-chr3:47321864..47324822,2	MCF-7	breast:
4	chr3:47016936..47018509-chr3:47322606..47324747,2	K562	blood:
5	chr3:47204122..47207133-chr3:47321636..47325818,4	K562	blood:

Variant related genes	Relation type
KIF9	TF binding region
KLHL18	TF binding region
ENSG00000260236	Chromatin interaction
ENSG00000088727	Chromatin interaction
ENSG00000227398	Chromatin interaction
ENSG00000160799	Chromatin interaction
ENSG00000181555	Chromatin interaction
ENSG00000076201	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1038394	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs10865946	0.96[CEU][hapmap]
rs11130115	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs11130123	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130124	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130126	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes]
rs11130128	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs11130129	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs11705957	0.96[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs11710013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11710121	0.92[ASW][hapmap];0.85[CEU][hapmap];0.84[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11710322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.98[ASN][1000 genomes]
rs11711824	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs11712445	0.96[CEU][hapmap]
rs11714294	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11716763	0.96[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap]
rs11719877	0.96[CEU][hapmap];0.80[GIH][hapmap];0.93[TSI][hapmap]
rs11915074	0.92[CEU][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes]
rs11920853	0.92[CEU][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes]
rs11921117	0.85[EUR][1000 genomes]
rs12636851	0.96[CEU][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs13061071	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs13072802	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13075233	0.96[CEU][hapmap];0.80[GIH][hapmap];0.93[TSI][hapmap]
rs13094438	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1466741	0.83[YRI][hapmap]
rs1531875	0.96[CEU][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs1638676	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];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17080872	0.81[JPT][hapmap]
rs17410853	0.85[CEU][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap]
rs17411375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs17476234	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1872164	0.96[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs2101247	0.92[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs2132173	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap]
rs2159400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap]
rs2276853	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2276854	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs295428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs295441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs295442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs295449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs295458	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]
rs295461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs3736177	0.96[CEU][hapmap]
rs4078466	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs4082155	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap]
rs4682852	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4683326	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858811	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs4858824	0.96[CEU][hapmap]
rs4858868	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs4858893	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs4858894	0.87[CEU][hapmap];0.88[JPT][hapmap]
rs59689369	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6767907	1.00[ASW][hapmap];0.81[CEU][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap]
rs6768221	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs6772670	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs6780013	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs6791842	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6792461	0.96[CEU][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs6800271	0.96[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs7636423	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7651762	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs807932	0.96[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];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs807935	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs807936	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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs807937	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs811115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs878659	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs922957	0.96[CEU][hapmap]
rs9311403	0.84[CEU][hapmap];0.86[YRI][hapmap]
rs9683033	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs9837343	1.00[ASW][hapmap];0.81[CEU][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1076394	CCDC12	cis	cerebellum	SCAN
rs1076394	NCKIPSD	cis	cerebellum	SCAN
rs1076394	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs1076394	HYAL2	cis	cerebellum	SCAN
rs1076394	RTP3	cis	lesional skin	skin_eQTL
rs1076394	C3orf75	cis	cerebellum	SCAN
rs1076394	PRKAR2A	cis	cerebellum	SCAN
rs1076394	AMIGO3	cis	cerebellum	SCAN
rs1076394	SCAP	cis	parietal	SCAN
rs1076394	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47293600-47323200	Weak transcription	Spleen	Spleen
2	chr3:47300800-47322800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:47301000-47322800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:47301200-47323000	Weak transcription	Psoas Muscle	Psoas
5	chr3:47302800-47323200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:47305600-47323200	Weak transcription	Primary T cells from cord blood	blood
7	chr3:47308600-47323000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:47308600-47323200	Weak transcription	Esophagus	oesophagus
9	chr3:47308800-47322800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:47308800-47322800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:47308800-47323000	Weak transcription	Adipose Nuclei	Adipose
12	chr3:47308800-47323000	Weak transcription	Brain Substantia Nigra	brain
13	chr3:47309000-47322800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:47309000-47322800	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:47309000-47323000	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:47309000-47323200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:47309000-47323200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:47309200-47323200	Weak transcription	HSMMtube	muscle
19	chr3:47311000-47322800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:47312400-47323000	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:47312600-47322800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr3:47314800-47323200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr3:47316200-47323000	Weak transcription	Fetal Stomach	stomach
24	chr3:47316200-47323200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:47317800-47323000	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:47321400-47323200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:47321800-47323000	Enhancers	Pancreas	Pancrea
28	chr3:47322200-47322800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:47322200-47322800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:47322200-47323000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:47322200-47323000	Enhancers	Gastric	stomach
32	chr3:47322200-47323000	Enhancers	Stomach Smooth Muscle	stomach
33	chr3:47322200-47323000	Enhancers	Dnd41	blood
34	chr3:47322200-47323200	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:47322200-47323200	Enhancers	GM12878-XiMat	blood
36	chr3:47322200-47323400	Enhancers	Lung	lung
37	chr3:47322400-47322800	Enhancers	Fetal Intestine Small	intestine
38	chr3:47322400-47322800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:47322400-47322800	Flanking Active TSS	HepG2	liver
40	chr3:47322400-47323000	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr3:47322400-47323000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:47322400-47323000	Enhancers	Placenta	Placenta
43	chr3:47322400-47323000	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr3:47322400-47323200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:47322400-47323200	Enhancers	Primary hematopoietic stem cells	blood
46	chr3:47322400-47323200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr3:47322400-47323200	Weak transcription	Aorta	Aorta
48	chr3:47322400-47323200	Weak transcription	Brain Germinal Matrix	brain
49	chr3:47322400-47323200	Enhancers	Right Ventricle	heart
50	chr3:47322400-47323200	Enhancers	Sigmoid Colon	Sigmoid Colon

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