Variant report

Variant	rs17418801
Chromosome Location	chr4:87414563-87414564
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87374448..87376940-chr4:87414111..87415663,2	MCF-7	breast:
2	chr4:87412697..87414960-chr4:87415593..87417580,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10008165	0.89[CHB][hapmap];0.92[GIH][hapmap];0.80[JPT][hapmap]
rs10023787	0.89[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap]
rs10029671	0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap]
rs10031843	0.94[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1021101	0.94[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap]
rs1026861	0.89[CHB][hapmap];0.87[GIH][hapmap]
rs11097115	0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1187211	1.00[YRI][hapmap]
rs11947018	0.84[GIH][hapmap]
rs11947775	0.97[ASN][1000 genomes]
rs1481833	0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap]
rs17011924	0.91[ASN][1000 genomes]
rs17418221	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17418531	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17418878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17419295	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs17419627	0.84[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap]
rs17419929	0.84[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap]
rs17452467	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17452556	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453839	0.94[CHB][hapmap]
rs28483710	0.80[ASN][1000 genomes]
rs28529445	0.81[ASN][1000 genomes]
rs4235081	0.93[ASN][1000 genomes]
rs4277747	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4404513	0.93[ASN][1000 genomes]
rs4405982	0.91[ASN][1000 genomes]
rs4407468	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4452393	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4466012	0.96[ASN][1000 genomes]
rs4511966	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4513526	0.80[ASN][1000 genomes]
rs4529013	0.95[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs4552430	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4607180	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4622964	0.91[ASN][1000 genomes]
rs4640633	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4693147	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];0.95[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693772	0.97[ASN][1000 genomes]
rs4693776	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4693777	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55653332	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55654230	0.83[ASN][1000 genomes]
rs55660529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55722156	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55746316	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55757426	0.84[ASN][1000 genomes]
rs55773619	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55814693	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55842318	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55872468	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55879246	0.84[ASN][1000 genomes]
rs55881335	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55908925	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55930543	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55969415	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55982489	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56009992	0.96[ASN][1000 genomes]
rs56150118	0.81[ASN][1000 genomes]
rs56164000	0.93[ASN][1000 genomes]
rs56178389	0.81[ASN][1000 genomes]
rs56222033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56296936	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56348925	0.86[ASN][1000 genomes]
rs56353461	0.93[ASN][1000 genomes]
rs59644743	0.91[ASN][1000 genomes]
rs61152200	0.91[ASN][1000 genomes]
rs6531932	0.89[CHB][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap]
rs67341369	0.84[ASN][1000 genomes]
rs67523832	0.83[ASN][1000 genomes]
rs67928053	0.80[ASN][1000 genomes]
rs6822396	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[ASN][1000 genomes]
rs6838659	0.95[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6847139	0.95[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs72664002	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72665711	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72665712	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72665714	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665719	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72665722	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72665724	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72665725	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72665729	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72665734	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72665736	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72665737	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72665738	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72665740	0.93[ASN][1000 genomes]
rs72665744	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72665746	0.93[ASN][1000 genomes]
rs72665752	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72665753	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72665756	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72665759	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72665762	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72665769	0.83[ASN][1000 genomes]
rs72665771	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72665772	0.81[ASN][1000 genomes]
rs7435744	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7673698	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7675845	0.89[ASN][1000 genomes]
rs7679269	0.83[ASN][1000 genomes]
rs7694723	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs7695011	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7697819	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9307020	0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap]
rs9683663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993042	0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17418801	HPSE	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87404600-87414800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:87405000-87418400	Weak transcription	Fetal Kidney	kidney
3	chr4:87405800-87414600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:87407000-87417000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:87407600-87422600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:87409400-87418400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:87411800-87417600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:87412400-87415000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:87412600-87418400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:87413000-87417000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:87413600-87414600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:87413600-87414800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:87413600-87415600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr4:87414000-87415200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr4:87414200-87415200	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr4:87414200-87415400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr4:87414400-87415400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:87414400-87415800	Enhancers	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links