Variant report

Variant	rs17080319
Chromosome Location	chr3:48732480-48732481
allele	C/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	YY1	chr3:48731949-48732563	SK-N-SH_RA	brain:	n/a	n/a
2	POLR2A	chr3:48732241-48732555	HCT-116	colon:	n/a	n/a
3	POLR2A	chr3:48731875-48732565	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr3:48732152-48733157	GM12892	blood:	n/a	n/a
5	EP300	chr3:48732001-48732503	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr3:48732111-48733278	H1-hESC	embryonic stem cell:	n/a	n/a
7	CHD2	chr3:48732251-48732492	Hela-S3	cervix:	n/a	n/a
8	USF2	chr3:48732162-48732505	Hela-S3	cervix:	n/a	n/a
9	MAX	chr3:48732028-48732586	SK-N-SH	brain:	n/a	n/a
10	NFIC	chr3:48731804-48732759	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr3:48732303-48733134	A549	lung:	n/a	n/a
12	STAT3	chr3:48732032-48732523	MCF10A-Er-Src	breast:	n/a	n/a
13	YY1	chr3:48732183-48732593	SK-N-SH_RA	brain:	n/a	n/a
14	CEBPB	chr3:48732054-48732591	A549	lung:	n/a	chr3:48732320-48732331
15	NFIC	chr3:48731962-48732734	ECC-1	luminal epithelium:	n/a	n/a
16	CEBPB	chr3:48731953-48732542	Hela-S3	cervix:	n/a	chr3:48732320-48732331
17	POLR2A	chr3:48732215-48733242	GM12891	blood:	n/a	n/a
18	MXI1	chr3:48731851-48732819	IMR90	lung:	n/a	n/a
19	TCF12	chr3:48731825-48732655	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr3:48731964-48733172	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:48732380-48733201	H1-hESC	embryonic stem cell:	n/a	n/a
22	CEBPB	chr3:48732091-48732591	ECC-1	luminal epithelium:	n/a	chr3:48732320-48732331
23	POLR2A	chr3:48732202-48733042	GM12891	blood:	n/a	n/a
24	POLR2A	chr3:48731983-48733135	U87	brain:	n/a	n/a
25	MAX	chr3:48732235-48732602	Hela-S3	cervix:	n/a	n/a
26	E2F4	chr3:48731963-48732538	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr3:48732304-48732679	HepG2	liver:	n/a	n/a
28	CEBPB	chr3:48732095-48732533	MCF-7	breast:	n/a	chr3:48732320-48732331
29	POLR2A	chr3:48732229-48732611	GM12892	blood:	n/a	n/a
30	CEBPB	chr3:48731959-48732563	HCT-116	colon:	n/a	chr3:48732320-48732331
31	MAZ	chr3:48732163-48732568	Hela-S3	cervix:	n/a	n/a
32	FOS	chr3:48731924-48732499	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr3:48732083-48733179	GM12878	blood:	n/a	n/a
34	NFIC	chr3:48732011-48732726	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr3:48732211-48733067	GM12891	blood:	n/a	n/a
36	CEBPB	chr3:48731833-48732678	HCT-116	colon:	n/a	chr3:48732320-48732331
37	RCOR1	chr3:48732214-48732504	Hela-S3	cervix:	n/a	n/a
38	MYC	chr3:48732047-48732528	MCF10A-Er-Src	breast:	n/a	n/a
39	MYC	chr3:48731929-48732617	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr3:48732026-48732749	HUVEC	blood vessel:	n/a	n/a
41	NFIC	chr3:48731868-48732641	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr3:48732334-48733016	H1-neurons	neurons:	n/a	n/a
43	POLR2A	chr3:48732074-48733145	HepG2	liver:	n/a	n/a
44	POLR2A	chr3:48732286-48732985	GM12878	blood:	n/a	n/a
45	POLR2A	chr3:48732253-48733079	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr3:48732248-48732697	Hela-S3	cervix:	n/a	n/a
47	MAZ	chr3:48731099-48733260	IMR90	lung:	n/a	n/a
48	POLR2A	chr3:48732282-48733231	H1-hESC	embryonic stem cell:	n/a	n/a
49	CEBPB	chr3:48732124-48732525	ECC-1	luminal epithelium:	n/a	chr3:48732320-48732331
50	SIN3AK20	chr3:48731988-48732506	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48699225..48701604-chr3:48731929..48734312,2	MCF-7	breast:
2	chr3:48720678..48725638-chr3:48726169..48732697,10	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TREX1-2	chr3:48731727-48732701	ENSG00000232483

Variant related genes	Relation type
IP6K2	TF binding region
ENSG00000008300	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000213672	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10865952	0.95[ASN][1000 genomes]
rs11557629	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706203	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713694	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs11715177	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715689	0.80[AMR][1000 genomes]
rs11715713	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11715835	0.81[ASN][1000 genomes]
rs11719291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719457	0.80[AMR][1000 genomes]
rs11928552	1.00[JPT][hapmap]
rs12107418	0.81[EUR][1000 genomes]
rs12493289	1.00[JPT][hapmap]
rs12493578	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12497850	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12715429	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13063223	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070798	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13074318	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs13076269	0.81[AMR][1000 genomes]
rs13086240	0.84[AMR][1000 genomes]
rs13090013	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090839	0.80[AMR][1000 genomes]
rs13091944	0.82[JPT][hapmap]
rs13096357	0.81[AMR][1000 genomes]
rs13316551	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324119	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13324950	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352420	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2286651	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2286652	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2302295	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28452701	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28567949	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28657585	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28793701	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34037363	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs34096717	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34153629	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34577723	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35064573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733086	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3806694	1.00[JPT][hapmap]
rs3821875	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4077495	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858798	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4858828	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4858831	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs56735597	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61137521	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6442130	1.00[CHB][hapmap]
rs6446253	0.82[JPT][hapmap]
rs6768448	0.85[EUR][1000 genomes]
rs6773261	0.81[AMR][1000 genomes]
rs6788650	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs68042649	0.85[EUR][1000 genomes]
rs73078362	0.81[EUR][1000 genomes]
rs7428949	1.00[JPT][hapmap]
rs7627404	1.00[CHB][hapmap]
rs7633840	0.86[ASN][1000 genomes]
rs9809222	0.85[EUR][1000 genomes]
rs9811027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811318	0.85[EUR][1000 genomes]
rs9812200	0.83[EUR][1000 genomes]
rs9812977	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9821797	0.85[EUR][1000 genomes]
rs9834996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835307	1.00[CHB][hapmap]
rs9836462	0.85[EUR][1000 genomes]
rs9841602	0.85[EUR][1000 genomes]
rs9848203	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9854034	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9873726	1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs9877542	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877685	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17080319	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs17080319	WDR6	cis	Whole Blood	GTEx
rs17080319	WDR6	cis	lung	GTEx
rs17080319	WDR6	cis	Esophagus Mucosa	GTEx
rs17080319	WDR6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48723800-48733800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:48724200-48732600	Strong transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:48724400-48735800	Strong transcription	GM12878-XiMat	blood
4	chr3:48724600-48733000	Strong transcription	Primary T cells from cord blood	blood
5	chr3:48724600-48734000	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr3:48724600-48734000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:48724600-48738000	Strong transcription	Thymus	Thymus
8	chr3:48724600-48738400	Strong transcription	Primary hematopoietic stem cells	blood
9	chr3:48724600-48740400	Strong transcription	Primary B cells from cord blood	blood
10	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
11	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:48724800-48732600	Strong transcription	Spleen	Spleen
13	chr3:48724800-48732800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:48724800-48733000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:48724800-48733000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:48724800-48733800	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:48724800-48733800	Strong transcription	HepG2	liver
18	chr3:48724800-48734000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:48724800-48735800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:48724800-48737600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:48724800-48738400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr3:48725000-48733200	Strong transcription	Liver	Liver
23	chr3:48725000-48738600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr3:48725000-48738600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:48725000-48740400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:48725000-48740800	Strong transcription	Dnd41	blood
27	chr3:48725200-48732800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:48725200-48733200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:48725200-48738600	Strong transcription	Primary B cells from peripheral blood	blood
30	chr3:48725200-48746200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:48725400-48733200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:48725800-48732600	Strong transcription	Fetal Muscle Leg	muscle
33	chr3:48727200-48733000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:48729800-48732800	Strong transcription	Small Intestine	intestine
35	chr3:48730000-48732600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr3:48730600-48732800	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
37	chr3:48730600-48733600	Weak transcription	K562	blood
38	chr3:48731000-48732800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:48731000-48732800	Transcr. at gene 5' and 3'	Left Ventricle	heart
40	chr3:48731000-48732800	Genic enhancers	Stomach Mucosa	stomach
41	chr3:48731000-48733000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
42	chr3:48731000-48733000	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
43	chr3:48731000-48733000	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
44	chr3:48731000-48733200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:48731000-48733200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:48731000-48733200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
47	chr3:48731000-48734000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr3:48731200-48732600	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:48731200-48735000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:48731400-48733000	Transcr. at gene 5' and 3'	HSMM	muscle

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