Variant report

Variant	rs7554019
Chromosome Location	chr1:114085723-114085724
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:114084981..114088872-chr1:114091176..114094977,3	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10858001	0.86[YRI][hapmap]
rs10858002	0.81[LWK][hapmap];0.86[YRI][hapmap]
rs11102651	0.85[LWK][hapmap];0.86[YRI][hapmap]
rs1217216	0.87[ASN][1000 genomes]
rs1217222	0.85[ASN][1000 genomes]
rs1217225	0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.87[ASN][1000 genomes]
rs1217231	0.89[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1343629	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1418957	0.81[YRI][hapmap]
rs17508449	0.80[CHD][hapmap]
rs2153977	0.81[LWK][hapmap]
rs35390985	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4259646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537790	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];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6704188	0.81[YRI][hapmap]
rs7514649	0.80[CHD][hapmap]
rs7522138	0.84[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]

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	nsv437013	chr1:114065955-114129092	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv946153	chr1:114080236-114088844	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7554019	BCL2L15	cis	cerebellum	SCAN
rs7554019	PHTF1	cis	cerebellum	SCAN
rs7554019	DCLRE1B	cis	cerebellum	SCAN
rs7554019	MAGI3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114072200-114095800	Weak transcription	Aorta	Aorta
2	chr1:114078000-114090000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:114080600-114088600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:114082400-114088400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:114082600-114100400	Weak transcription	Fetal Kidney	kidney
6	chr1:114083200-114099800	Weak transcription	Pancreas	Pancrea
7	chr1:114083400-114095200	Weak transcription	Liver	Liver
8	chr1:114083400-114100000	Weak transcription	Ovary	ovary
9	chr1:114083400-114110000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:114084000-114092000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:114084200-114088600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:114084600-114089800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:114084800-114095200	Weak transcription	Fetal Intestine Large	intestine
14	chr1:114084800-114095600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:114085000-114092400	Weak transcription	Fetal Intestine Small	intestine
16	chr1:114085200-114088000	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:114085400-114085800	Enhancers	NHEK	skin
18	chr1:114085600-114087000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:114085600-114093600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:114085600-114094000	Weak transcription	HMEC	breast
21	chr1:114085600-114094200	Weak transcription	NHDF-Ad	bronchial
22	chr1:114085600-114101800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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