Variant report

Variant	rs4680449
Chromosome Location	chr3:158350118-158350119
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1038886	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1047366	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1075551	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936158	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12107643	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496174	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12639052	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13074694	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13324770	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13325932	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1369563	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1435642	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1435643	0.85[CHB][hapmap]
rs1595028	0.95[CHB][hapmap]
rs1602760	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1620229	0.90[ASN][1000 genomes]
rs1656366	0.95[CHB][hapmap]
rs1656376	0.95[CHB][hapmap]
rs1656377	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs1714507	0.95[CHB][hapmap]
rs1714516	0.90[ASN][1000 genomes]
rs1714518	0.95[CHB][hapmap]
rs17629360	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17629390	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17629414	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17630086	0.85[CHB][hapmap]
rs17699456	0.83[CEU][hapmap]
rs1836688	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1864503	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1864507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2115943	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2248924	0.99[ASN][1000 genomes]
rs2276773	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2303909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2364274	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2566344	0.97[ASN][1000 genomes]
rs2573179	0.97[ASN][1000 genomes]
rs2731112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2731118	0.97[ASN][1000 genomes]
rs2731120	0.93[ASN][1000 genomes]
rs2731122	0.91[ASN][1000 genomes]
rs28481597	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2933550	0.96[ASN][1000 genomes]
rs3765025	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3845272	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3851361	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851362	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs3851363	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680445	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680450	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680451	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680452	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680453	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680457	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680460	0.84[CEU][hapmap]
rs4875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62287933	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441206	0.95[CHB][hapmap]
rs6441212	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441220	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6763812	0.88[ASN][1000 genomes]
rs6771248	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6772483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6777711	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6781342	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6783879	0.84[CEU][hapmap]
rs6795376	0.95[CHB][hapmap]
rs6800914	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6802317	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6803047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6803608	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6804249	0.84[CEU][hapmap]
rs6804259	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7609717	0.82[AMR][1000 genomes]
rs7612250	0.85[CHB][hapmap]
rs7613814	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7613824	0.85[CHB][hapmap]
rs7620927	0.95[CHB][hapmap]
rs7621897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7628293	0.85[CHB][hapmap]
rs7631310	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7648618	0.90[CHB][hapmap]
rs7653826	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs891464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9810887	0.90[CHB][hapmap]
rs9819134	0.90[CHB][hapmap]
rs9819567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9819631	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9824985	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9840571	0.84[CEU][hapmap]
rs9844502	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9848908	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9858318	0.90[CHB][hapmap]
rs9859129	0.90[CHB][hapmap]
rs9864508	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9866134	0.84[CEU][hapmap]
rs9883657	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv877691	chr3:158245883-158359667	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv869644	chr3:158308783-158426343	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	esv999299	chr3:158348460-158358157	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region	2 gene(s)	inside rSNPs	diseases
9	esv3461211	chr3:158348758-158353756	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region	1 gene(s)	inside rSNPs	diseases
10	esv2518941	chr3:158349755-158352064	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases
11	esv3461213	chr3:158349783-158353131	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases
12	esv3450832	chr3:158350108-158352906	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4680449	LXN	cis	parietal	SCAN
rs4680449	LXN	cis	cerebellum	SCAN
rs4680449	LXN	cis	multi-tissue	Pritchard
rs4680449	MLF1	cis	Esophagus Mucosa	GTEx
rs4680449	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs4680449	LXN	cis	lymphoblastoid	seeQTL
rs4680449	SNRNP27	trans	parietal	SCAN
rs4680449	SSR3	cis	parietal	SCAN
rs4680449	MLF1	cis	Heart Left Ventricle	GTEx
rs4680449	GFM1	cis	cerebellum	SCAN
rs4680449	GFM1	cis	parietal	SCAN
rs4680449	IQCJ	cis	parietal	SCAN
rs4680449	RARRES1	cis	cerebellum	SCAN
rs4680449	GFM1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158349000-158351800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:158349400-158351400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:158349600-158350200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr3:158349600-158350200	Enhancers	Brain Germinal Matrix	brain
5	chr3:158349600-158350400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:158349600-158350400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:158349600-158350600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:158349800-158350200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr3:158349800-158350200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:158349800-158350200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr3:158349800-158350200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr3:158349800-158350600	Enhancers	H9 Cell Line	embryonic stem cell
13	chr3:158350000-158350200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:158350000-158350400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:158350000-158350400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:158350000-158350600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr3:158350000-158350600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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