Variant report

Variant	rs3813639
Chromosome Location	chr1:179050478-179050479
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	POLR2A	chr1:179050421-179053208	GM12892	blood:	n/a	n/a
2	TCF12	chr1:179050456-179052398	A549	lung:	n/a	n/a
3	TEAD4	chr1:179050389-179051453	K562	blood:	n/a	n/a
4	NFIC	chr1:179050470-179051159	GM12878	blood:	n/a	n/a
5	CEBPB	chr1:179050376-179051220	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:179049925-179052426	GM12878	blood:	n/a	n/a
7	MAZ	chr1:179050435-179052538	IMR90	lung:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708
8	FOSL2	chr1:179050471-179051311	HepG2	liver:	n/a	n/a
9	MTA3	chr1:179050015-179052498	GM12878	blood:	n/a	n/a
10	SIN3AK20	chr1:179050408-179052408	MCF-7	breast:	n/a	n/a
11	RELA	chr1:179050239-179051560	GM18951	blood:	n/a	chr1:179050571-179050580 chr1:179050571-179050580
12	RUNX3	chr1:179049989-179051669	GM12878	blood:	n/a	n/a
13	RELA	chr1:179050164-179051395	GM10847	blood:	n/a	chr1:179050571-179050580 chr1:179050571-179050580
14	MYC	chr1:179050372-179052402	K562	blood:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708
15	STAT3	chr1:179050403-179051103	GM12878	blood:	n/a	chr1:179051001-179051010 chr1:179050674-179050685 chr1:179051000-179051009 chr1:179050999-179051010
16	POLR2A	chr1:179050354-179051514	GM12891	blood:	n/a	n/a
17	POLR2A	chr1:179049821-179052584	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:179049868-179052441	Hela-S3	cervix:	n/a	n/a
19	ATF2	chr1:179050378-179051346	GM12878	blood:	n/a	n/a
20	NFIC	chr1:179049994-179051379	GM12878	blood:	n/a	n/a
21	E2F4	chr1:179050457-179051375	MCF10A-Er-Src	breast:	n/a	chr1:179051077-179051088 chr1:179050827-179050839
22	POLR2A	chr1:179050074-179051628	GM12878	blood:	n/a	n/a
23	SMARCB1	chr1:179050430-179052306	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr1:179050072-179053327	GM19193	blood:	n/a	n/a
25	POLR2A	chr1:179049835-179053382	GM12891	blood:	n/a	n/a
26	MAX	chr1:179050405-179051289	H1-hESC	embryonic stem cell:	n/a	chr1:179050699-179050708
27	STAT5A	chr1:179050421-179051598	GM12878	blood:	n/a	chr1:179051120-179051132 chr1:179051001-179051010 chr1:179050674-179050685 chr1:179051000-179051009
28	MAX	chr1:179050464-179052634	A549	lung:	n/a	chr1:179051658-179051668 chr1:179052196-179052205 chr1:179050699-179050708
29	BHLHE40	chr1:179050474-179051575	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:179050469-179052311	Hela-S3	cervix:	n/a	n/a
31	MXI1	chr1:179050215-179052309	GM12878	blood:	n/a	chr1:179051135-179051150
32	POLR2A	chr1:179049961-179051624	K562	blood:	n/a	n/a
33	POLR2A	chr1:179050383-179052611	GM12892	blood:	n/a	n/a
34	SPI1	chr1:179050383-179051422	GM12878	blood:	n/a	chr1:179050619-179050626 chr1:179050618-179050627 chr1:179050814-179050821 chr1:179050676-179050685
35	POLR2A	chr1:179050436-179052175	K562	blood:	n/a	n/a
36	HA-E2F1	chr1:179050446-179052407	MCF-7	breast:	n/a	chr1:179051662-179051672 chr1:179050827-179050839 chr1:179051754-179051763
37	SPI1	chr1:179050472-179051313	GM12891	blood:	n/a	chr1:179050619-179050626 chr1:179050618-179050627 chr1:179050814-179050821 chr1:179050676-179050685
38	POLR2A	chr1:179050443-179052418	H1-hESC	embryonic stem cell:	n/a	n/a
39	MXI1	chr1:179050359-179052274	HepG2	liver:	n/a	chr1:179051135-179051150
40	WRNIP1	chr1:179049959-179051071	GM12878	blood:	n/a	n/a
41	SPI1	chr1:179050473-179050893	GM12878	blood:	n/a	chr1:179050619-179050626 chr1:179050618-179050627 chr1:179050814-179050821 chr1:179050676-179050685
42	UBTF	chr1:179050250-179052411	K562	blood:	n/a	n/a
43	CHD2	chr1:179050438-179051371	GM12878	blood:	n/a	n/a
44	SIN3A	chr1:179050336-179051439	GM12878	blood:	n/a	chr1:179051055-179051069
45	NFATC1	chr1:179050173-179051196	GM12878	blood:	n/a	chr1:179050640-179050654
46	POLR2A	chr1:179049785-179051561	K562	blood:	n/a	n/a
47	RELA	chr1:179050384-179051643	GM19193	blood:	n/a	chr1:179050571-179050580 chr1:179050571-179050580
48	ELF1	chr1:179050418-179051501	MCF-7	breast:	n/a	chr1:179050813-179050824
49	TBL1XR1	chr1:179050380-179051390	GM12878	blood:	n/a	n/a
50	POLR2A	chr1:179049829-179053345	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:179049954..179052769-chr1:179333565..179337813,7	MCF-7	breast:
2	chr1:178837797..178839494-chr1:179049948..179052882,2	K562	blood:
3	chr1:178993182..178999783-chr1:179045102..179052535,14	MCF-7	breast:
4	chr1:179048972..179052099-chr1:179331450..179336701,5	MCF-7	breast:
5	chr1:179049424..179053663-chr1:179259743..179264339,5	MCF-7	breast:
6	chr1:179049160..179052033-chr1:179333339..179335895,3	K562	blood:

Variant related genes	Relation type
TOR3A	TF binding region
ENSG00000057252	Chromatin interaction
ENSG00000162779	Chromatin interaction
ENSG00000263633	Chromatin interaction
ENSG00000116199	Chromatin interaction
ENSG00000116194	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs16853590	0.86[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs16853612	0.86[CEU][hapmap];0.80[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16853647	0.90[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs2018786	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2147769	0.80[CHB][hapmap];0.82[TSI][hapmap]
rs2296376	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766623	0.86[CEU][hapmap];0.80[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3766625	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3766629	0.86[CEU][hapmap];0.80[CHB][hapmap];0.82[AMR][1000 genomes]
rs3766630	0.82[AMR][1000 genomes]
rs3766635	0.86[CEU][hapmap];0.80[CHB][hapmap];0.81[TSI][hapmap]
rs3813640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs429931	0.80[CHB][hapmap];1.00[YRI][hapmap]
rs45628232	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55854504	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56006430	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56032836	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56173043	0.82[AMR][1000 genomes]
rs56999658	0.82[AMR][1000 genomes]
rs57601259	0.84[AFR][1000 genomes]
rs67939704	0.82[ASN][1000 genomes]
rs72709419	0.82[AMR][1000 genomes]
rs72709423	0.82[AMR][1000 genomes]
rs72709441	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72709445	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72709448	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7527432	0.82[TSI][hapmap]
rs9249	0.86[CEU][hapmap];0.80[CHB][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3813639	KIAA0040	cis	parietal	SCAN
rs3813639	FAM20B	cis	cerebellum	SCAN
rs3813639	TNR	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179025400-179050600	Weak transcription	Fetal Brain Male	brain
2	chr1:179027800-179050600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:179028600-179050600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:179036200-179050800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:179041600-179050600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:179041600-179050600	Weak transcription	Lung	lung
7	chr1:179041800-179050600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:179041800-179050600	Weak transcription	Aorta	Aorta
9	chr1:179042400-179050600	Weak transcription	Ovary	ovary
10	chr1:179043200-179050600	Weak transcription	Fetal Brain Female	brain
11	chr1:179048200-179050600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:179048400-179050600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:179049800-179050600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr1:179049800-179050800	Flanking Active TSS	Liver	Liver
15	chr1:179049800-179051000	Flanking Active TSS	GM12878-XiMat	blood
16	chr1:179049800-179051200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr1:179050000-179050600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:179050000-179050600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:179050000-179050600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:179050000-179050600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:179050000-179050600	Flanking Active TSS	Colonic Mucosa	Colon
22	chr1:179050000-179050600	Enhancers	Esophagus	oesophagus
23	chr1:179050000-179050600	Enhancers	Fetal Intestine Small	intestine
24	chr1:179050000-179050600	Enhancers	Fetal Lung	lung
25	chr1:179050000-179050600	Enhancers	Fetal Thymus	thymus
26	chr1:179050000-179050600	Enhancers	Gastric	stomach
27	chr1:179050000-179050600	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr1:179050000-179050800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:179050000-179050800	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr1:179050000-179050800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr1:179050000-179050800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr1:179050000-179050800	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr1:179050000-179051000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:179050000-179051000	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr1:179050000-179051000	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr1:179050000-179051000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:179050000-179051000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr1:179050000-179051000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr1:179050000-179051000	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr1:179050000-179051000	Flanking Active TSS	Hela-S3	cervix
41	chr1:179050200-179050600	Enhancers	H1 Cell Line	embryonic stem cell
42	chr1:179050200-179050600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:179050200-179050600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:179050200-179050600	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr1:179050200-179050600	Enhancers	Primary hematopoietic stem cells	blood
46	chr1:179050200-179050600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr1:179050200-179050600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:179050200-179050600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:179050200-179050600	Flanking Active TSS	Colon Smooth Muscle	Colon
50	chr1:179050200-179050600	Enhancers	Fetal Heart	heart

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