Variant report

Variant	rs7172159
Chromosome Location	chr15:92506614-92506615
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:92501600..92503533-chr15:92506006..92508030,3	MCF-7	breast:
2	chr15:92495489..92497057-chr15:92505044..92507956,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10454699	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs10852164	0.81[CEU][hapmap];0.90[CHD][hapmap];0.88[MEX][hapmap]
rs10852165	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10852166	0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs11635055	0.81[CHB][hapmap]
rs12439826	0.82[ASN][1000 genomes]
rs12902685	0.85[CHB][hapmap]
rs12903803	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs12905744	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12909480	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs12910715	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs12910862	0.85[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs1356417	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1568210	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.80[JPT][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16946157	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16946164	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16946168	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2138849	0.81[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap]
rs2176452	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.86[LWK][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs28470895	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28513490	0.91[ASN][1000 genomes]
rs28752332	0.89[ASN][1000 genomes]
rs4312282	0.81[CHB][hapmap]
rs4932592	0.86[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs4932593	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61155306	0.84[ASN][1000 genomes]
rs7165760	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7171131	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7172099	0.88[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap]
rs7178673	0.96[ASN][1000 genomes]
rs7178734	0.94[EUR][1000 genomes]
rs7179815	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8025507	0.96[ASN][1000 genomes]
rs8027160	0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.91[ASN][1000 genomes]
rs8040046	0.88[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap]
rs953888	0.81[CHB][hapmap];0.83[CHD][hapmap];0.80[JPT][hapmap]
rs976216	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9920069	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048635	chr15:92073294-92557339	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv870094	chr15:92367354-92631647	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv534110	chr15:92397220-92592961	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7172159	SEMA4B	cis	parietal	SCAN
rs7172159	ZNF710	cis	parietal	SCAN
rs7172159	FANCI	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92498200-92555000	Weak transcription	Gastric	stomach
2	chr15:92500200-92509600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:92500800-92508600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:92500800-92508800	Weak transcription	Ovary	ovary
5	chr15:92504800-92507400	Weak transcription	Hela-S3	cervix
6	chr15:92504800-92507800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:92504800-92508200	Weak transcription	Brain Substantia Nigra	brain
8	chr15:92505000-92507200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:92505000-92507600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:92505000-92507600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:92505000-92507600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:92505000-92507600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:92505000-92508000	Weak transcription	A549	lung
14	chr15:92505200-92507200	Weak transcription	HMEC	breast
15	chr15:92505200-92507200	Weak transcription	NHEK	skin
16	chr15:92505200-92508200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr15:92505400-92507200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:92505800-92507000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:92506000-92507800	Weak transcription	Esophagus	oesophagus
20	chr15:92506000-92507800	Weak transcription	Left Ventricle	heart
21	chr15:92506000-92508000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:92506000-92508000	Weak transcription	Brain Angular Gyrus	brain
23	chr15:92506000-92508000	Weak transcription	Spleen	Spleen
24	chr15:92506000-92508800	Weak transcription	Lung	lung
25	chr15:92506000-92509000	Weak transcription	Placenta	Placenta
26	chr15:92506000-92513600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr15:92506000-92517600	Weak transcription	Colonic Mucosa	Colon
28	chr15:92506200-92507400	Weak transcription	Brain Hippocampus Middle	brain
29	chr15:92506200-92507600	Weak transcription	Right Ventricle	heart
30	chr15:92506200-92507800	Weak transcription	Aorta	Aorta
31	chr15:92506200-92507800	Weak transcription	Right Atrium	heart
32	chr15:92506200-92508200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr15:92506400-92507600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:92506400-92507600	Weak transcription	Fetal Heart	heart
35	chr15:92506400-92508000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr15:92506400-92508400	Weak transcription	Adipose Nuclei	Adipose
37	chr15:92506400-92508600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:92506600-92507800	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links