Variant report

Variant	rs10519977
Chromosome Location	chr5:127316801-127316802
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:127316343..127317135-chr5:127372728..127373541,2	MCF-7	breast:
2	chr5:127315555..127317396-chr5:127416978..127419162,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245937	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10040931	0.82[CEU][hapmap]
rs10052149	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10055964	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10057048	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10059403	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10076010	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10463835	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10463836	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10478786	0.80[EUR][1000 genomes]
rs10478787	0.85[CEU][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs10478788	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10478790	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10478791	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10478792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10519968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745009	0.81[EUR][1000 genomes]
rs11745023	0.81[CEU][hapmap]
rs12523625	0.85[CEU][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs13154863	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13161109	0.87[EUR][1000 genomes]
rs13167871	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13169878	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13174053	0.80[EUR][1000 genomes]
rs13177354	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13180050	0.81[EUR][1000 genomes]
rs13184942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1558149	0.85[CEU][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs17606751	0.92[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2041143	0.82[CEU][hapmap]
rs2108652	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2108654	0.80[EUR][1000 genomes]
rs34498802	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35673135	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35713319	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4141241	0.84[JPT][hapmap]
rs4836352	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4836354	0.93[ASN][1000 genomes]
rs5008451	0.89[CEU][hapmap]
rs59634534	0.80[EUR][1000 genomes]
rs6867103	0.87[CEU][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6867442	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6867465	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6867644	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6881456	0.80[EUR][1000 genomes]
rs6889393	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6892704	0.85[CEU][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs6897353	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732235	0.80[EUR][1000 genomes]
rs732236	0.85[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs7444438	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7719691	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7723104	0.84[JPT][hapmap]
rs7732912	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9327460	0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9327461	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9327462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10519977	SLC27A6	cis	parietal	SCAN
rs10519977	SLC12A2	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127290600-127332000	Weak transcription	Aorta	Aorta
2	chr5:127295800-127322800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:127296200-127322600	Weak transcription	Colon Smooth Muscle	Colon
4	chr5:127297600-127332000	Weak transcription	Primary B cells from cord blood	blood
5	chr5:127297800-127323200	Weak transcription	Gastric	stomach
6	chr5:127297800-127323600	Weak transcription	HSMMtube	muscle
7	chr5:127297800-127358400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr5:127302400-127321600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:127302400-127323400	Weak transcription	Fetal Stomach	stomach
10	chr5:127302600-127322800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:127304000-127333400	Weak transcription	Primary T cells from cord blood	blood
12	chr5:127306600-127333200	Weak transcription	Psoas Muscle	Psoas
13	chr5:127306800-127318400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:127306800-127323200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:127306800-127323200	Weak transcription	Left Ventricle	heart
16	chr5:127306800-127323200	Weak transcription	NHEK	skin
17	chr5:127312800-127318000	Enhancers	Stomach Mucosa	stomach
18	chr5:127312800-127323200	Weak transcription	NHLF	lung
19	chr5:127313400-127317200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:127316000-127317400	Enhancers	A549	lung
21	chr5:127316600-127317000	Enhancers	Pancreas	Pancrea
22	chr5:127316800-127318000	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links