Variant report

Variant	rs4560329
Chromosome Location	chr3:51193805-51193806
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10212250	0.91[CEU][hapmap]
rs10433609	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10446473	0.81[EUR][1000 genomes]
rs11130274	0.91[CEU][hapmap]
rs11130280	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130282	0.91[CEU][hapmap]
rs11130283	0.83[EUR][1000 genomes]
rs11130286	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11130290	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs11706571	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11711643	0.84[EUR][1000 genomes]
rs12491206	0.83[CHD][hapmap]
rs12494165	0.82[ASW][hapmap]
rs12496621	0.84[CHD][hapmap]
rs13061003	0.88[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap]
rs13064149	0.83[EUR][1000 genomes]
rs13080170	0.88[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1318649	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap]
rs1383252	0.91[CEU][hapmap]
rs1480353	0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap]
rs1480357	0.91[CEU][hapmap]
rs1480358	0.91[CEU][hapmap]
rs1480360	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs1480362	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1480363	0.91[CEU][hapmap]
rs1480364	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs1552072	0.91[CEU][hapmap]
rs1552073	0.91[CEU][hapmap]
rs2061950	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs2061951	0.91[CEU][hapmap]
rs2170178	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs2219890	0.81[CHB][hapmap];0.83[CHD][hapmap];0.91[MEX][hapmap]
rs2219891	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2291162	0.83[EUR][1000 genomes]
rs2355941	0.91[CEU][hapmap]
rs2355943	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs2355945	0.81[EUR][1000 genomes]
rs28708817	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28810453	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2883809	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35356497	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3856932	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4244697	0.91[CEU][hapmap]
rs4301044	0.91[CEU][hapmap]
rs4323036	0.84[CHD][hapmap]
rs4328835	0.90[CEU][hapmap]
rs4356848	0.94[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4364203	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4367100	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4367101	0.91[CEU][hapmap]
rs4378999	0.91[CEU][hapmap]
rs4434173	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4443210	0.94[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs4453876	0.91[CEU][hapmap]
rs4475072	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4528983	0.91[CEU][hapmap]
rs4532165	0.91[CEU][hapmap]
rs4538365	1.00[CEU][hapmap]
rs4557148	1.00[CEU][hapmap]
rs4568177	0.91[CEU][hapmap]
rs4572801	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4927961	0.84[CHD][hapmap]
rs4927969	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4927970	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4927973	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4974092	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4974094	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs4974095	0.91[CEU][hapmap]
rs4974099	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs4974104	0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap]
rs4974108	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs4974109	0.91[CEU][hapmap]
rs62257481	0.83[EUR][1000 genomes]
rs62257499	0.81[EUR][1000 genomes]
rs6445455	0.91[CEU][hapmap]
rs6445501	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6445549	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6445551	0.91[CEU][hapmap]
rs6445601	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6445604	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs6445611	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs6446243	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs6446245	0.94[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs6772197	0.88[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6772664	0.91[CEU][hapmap]
rs6777719	0.91[CEU][hapmap]
rs6779658	0.91[CEU][hapmap]
rs6783235	0.83[EUR][1000 genomes]
rs6784455	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6787805	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6795272	0.82[ASW][hapmap]
rs6796642	0.85[ASN][1000 genomes]
rs6796847	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6799722	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6809080	0.89[CEU][hapmap]
rs7427006	0.91[CEU][hapmap]
rs7614317	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7614482	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap]
rs7616967	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs7618173	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619584	0.91[CEU][hapmap]
rs7628533	0.91[CEU][hapmap]
rs7630714	1.00[CEU][hapmap]
rs7630730	0.91[CEU][hapmap]
rs7633708	0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap]
rs7634799	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7638732	0.82[ASW][hapmap]
rs7640083	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7644957	0.91[CEU][hapmap]
rs7648012	0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap]
rs7649069	0.94[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap]
rs7651141	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs899750	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs922612	0.91[CEU][hapmap]
rs9815781	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9832672	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9839484	0.89[ASN][1000 genomes]
rs9844581	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9847479	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9855442	0.91[CEU][hapmap]
rs9855454	0.82[CEU][hapmap]
rs9856566	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9857598	0.83[EUR][1000 genomes]
rs9858412	0.91[CEU][hapmap]
rs9860403	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs9865532	0.88[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9869123	0.89[CEU][hapmap]
rs9871539	0.91[CEU][hapmap]
rs9877188	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs9878100	0.91[CEU][hapmap]
rs9883739	0.91[CEU][hapmap]
rs995543	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][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	nsv491647	chr3:50856276-51245158	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4560329	TNNC1	cis	cerebellum	SCAN
rs4560329	MST1	cis	cerebellum	SCAN
rs4560329	HEMK1	cis	Lymphoblastoid	GTEx
rs4560329	HEMK1	cis	cerebellum	SCAN
rs4560329	PARP3	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51168200-51210600	Weak transcription	Brain Angular Gyrus	brain
2	chr3:51182200-51197800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:51183000-51209600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:51183400-51206800	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:51188800-51210600	Weak transcription	Brain Anterior Caudate	brain
6	chr3:51189600-51206800	Weak transcription	Fetal Brain Female	brain
7	chr3:51190400-51205800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:51190800-51203200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:51192600-51208800	Weak transcription	Brain Germinal Matrix	brain
10	chr3:51193200-51209800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:51193600-51209800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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