Variant report

Variant	rs7673698
Chromosome Location	chr4:87406566-87406567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10008165	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap]
rs10023787	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10029671	0.89[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs10031843	0.89[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1021101	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11097115	0.89[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs11943428	0.80[ASN][1000 genomes]
rs11947018	0.84[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap]
rs11947775	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1481833	0.89[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs17011924	0.94[ASN][1000 genomes]
rs17418221	0.89[ASN][1000 genomes]
rs17418531	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17418801	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17418878	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17419295	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs17419627	0.85[JPT][hapmap]
rs17452467	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17452556	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28483710	0.83[ASN][1000 genomes]
rs28529445	0.80[ASN][1000 genomes]
rs4235081	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4277747	0.86[ASN][1000 genomes]
rs4404513	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4405982	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4407468	0.93[ASN][1000 genomes]
rs4452393	0.91[ASN][1000 genomes]
rs4466012	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4511966	0.91[ASN][1000 genomes]
rs4513526	0.83[ASN][1000 genomes]
rs4529013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4552430	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4607180	0.93[ASN][1000 genomes]
rs4622964	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4640633	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4693147	0.95[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4693772	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693776	0.93[ASN][1000 genomes]
rs4693777	0.91[ASN][1000 genomes]
rs55653332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55654230	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs55660529	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs55722156	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55746316	0.83[ASN][1000 genomes]
rs55757426	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs55773619	0.83[ASN][1000 genomes]
rs55814693	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs55842318	0.93[ASN][1000 genomes]
rs55872468	0.93[ASN][1000 genomes]
rs55879246	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs55881335	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs55908925	0.93[ASN][1000 genomes]
rs55930543	0.93[ASN][1000 genomes]
rs55969415	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs55982489	0.93[ASN][1000 genomes]
rs56009992	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56150118	0.80[ASN][1000 genomes]
rs56164000	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56178389	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56222033	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs56296936	0.83[ASN][1000 genomes]
rs56348925	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56353461	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59644743	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61152200	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6531932	0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs67341369	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs67523832	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs67928053	0.83[ASN][1000 genomes]
rs6822396	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6838659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72664002	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72665711	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665712	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665714	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665719	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72665722	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72665724	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72665725	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72665729	0.93[ASN][1000 genomes]
rs72665734	0.93[ASN][1000 genomes]
rs72665736	0.93[ASN][1000 genomes]
rs72665737	0.93[ASN][1000 genomes]
rs72665738	0.93[ASN][1000 genomes]
rs72665740	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72665744	0.93[ASN][1000 genomes]
rs72665746	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72665752	0.93[ASN][1000 genomes]
rs72665753	0.91[ASN][1000 genomes]
rs72665756	0.91[ASN][1000 genomes]
rs72665759	0.85[ASN][1000 genomes]
rs72665762	0.85[ASN][1000 genomes]
rs72665769	0.86[ASN][1000 genomes]
rs72665771	0.83[ASN][1000 genomes]
rs72665772	0.80[ASN][1000 genomes]
rs7435744	0.91[ASN][1000 genomes]
rs7675845	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7679269	0.86[ASN][1000 genomes]
rs7694723	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs7695011	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697819	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9307020	0.89[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs9683663	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9993042	0.89[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.80[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7673698	PTPN13	cis	parietal	SCAN
rs7673698	HPSE	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87400800-87406800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:87403400-87407200	Enhancers	Dnd41	blood
3	chr4:87404000-87406800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr4:87404600-87407000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:87404600-87407000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr4:87404600-87414800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:87405000-87407200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:87405000-87418400	Weak transcription	Fetal Kidney	kidney
9	chr4:87405800-87407000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:87405800-87411400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:87405800-87412400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:87405800-87413600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:87405800-87414600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:87406000-87406800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:87406400-87407000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:87406400-87407200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr4:87406400-87408200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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