Variant report

Variant	rs6676785
Chromosome Location	chr1:173145017-173145018
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	SPI1	chr1:173144864-173145216	HL-60	blood:	n/a	chr1:173145125-173145132
2	POLR2A	chr1:173144973-173145087	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:173144643-173145348	HUVEC	blood vessel:	n/a	n/a
4	SETDB1	chr1:173144648-173145204	U2OS	brain:	n/a	n/a
5	STAT3	chr1:173144731-173145042	MCF10A-Er-Src	breast:	n/a	chr1:173144848-173144856

Variant related genes	Relation type
ENSG00000226375	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10127495	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10157163	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10158467	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912553	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10912554	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912555	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912556	1.00[JPT][hapmap]
rs10912564	0.86[CEU][hapmap];0.90[CHB][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs11811788	0.84[ASN][1000 genomes]
rs11811856	0.82[CEU][hapmap]
rs16845543	0.82[JPT][hapmap]
rs16845585	0.82[JPT][hapmap]
rs3861950	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4081545	0.90[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4090391	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916311	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916312	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916313	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56028318	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61826341	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661173	0.82[JPT][hapmap]
rs6665456	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691738	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7514229	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7518045	0.82[JPT][hapmap]
rs7518129	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7521390	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525284	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7553711	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6676785	FMO1	cis	cerebellum	SCAN
rs6676785	TNN	cis	parietal	SCAN
rs6676785	PPP1R2	trans	cerebellum	SCAN
rs6676785	TNFSF18	cis	cerebellum	SCAN
rs6676785	TNFSF18	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173132200-173158800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:173142400-173150800	Weak transcription	HSMMtube	muscle
3	chr1:173143000-173150600	Weak transcription	HSMM	muscle
4	chr1:173143000-173159000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:173144200-173146000	Enhancers	Primary B cells from cord blood	blood
6	chr1:173144400-173145600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:173144600-173145200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:173144600-173145200	Enhancers	Primary B cells from peripheral blood	blood
9	chr1:173144600-173145400	Enhancers	Primary hematopoietic stem cells	blood
10	chr1:173144600-173145400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:173144800-173145400	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links