Variant report

Variant	rs11961316
Chromosome Location	chr6:45029598-45029599
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10456120	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10456121	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456122	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10456542	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10456543	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs10456546	0.81[AMR][1000 genomes]
rs10456548	0.81[AMR][1000 genomes]
rs10456549	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10484626	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10948176	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10948196	1.00[JPT][hapmap]
rs10948201	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948204	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10948205	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10948211	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10948212	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10948213	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10948214	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10948216	0.82[AMR][1000 genomes]
rs10948217	0.81[AMR][1000 genomes]
rs11965706	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11967630	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11970412	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190313	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12190367	0.82[AMR][1000 genomes]
rs12191262	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12191521	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191566	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12192890	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs12193030	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs12193682	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12193720	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12193812	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12196188	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12196217	0.81[AMR][1000 genomes]
rs12198308	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12198376	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12198982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12201005	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12202232	0.81[AMR][1000 genomes]
rs12202434	0.81[AMR][1000 genomes]
rs12205379	0.81[AMR][1000 genomes]
rs12205860	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12205905	0.81[AMR][1000 genomes]
rs12206561	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs12206568	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12208332	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12208523	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12208605	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12209161	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12210292	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12211519	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12212190	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12212745	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12213735	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12214885	0.81[AMR][1000 genomes]
rs12215263	1.00[CHB][hapmap]
rs1324536	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1329709	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1329711	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17209636	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17209678	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17288250	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs17288257	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17423748	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1853651	0.81[AMR][1000 genomes]
rs2038765	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2093900	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs2396379	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34455867	0.82[ASN][1000 genomes]
rs3997499	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs56283067	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56337964	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56357385	0.81[AMR][1000 genomes]
rs56397204	0.81[AMR][1000 genomes]
rs62400267	0.81[AMR][1000 genomes]
rs62400268	0.81[AMR][1000 genomes]
rs62400269	0.81[AMR][1000 genomes]
rs62400289	0.81[AMR][1000 genomes]
rs62400290	0.81[AMR][1000 genomes]
rs62436760	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62436778	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62436779	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62436780	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62436781	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62436782	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62438863	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62438864	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438867	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438877	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908606	0.88[ASN][1000 genomes]
rs6909047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6919813	0.86[CEU][hapmap];0.82[AMR][1000 genomes]
rs6919873	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6919998	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6920046	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6924185	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6927213	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs72857080	0.81[AMR][1000 genomes]
rs72869118	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72869127	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72870950	0.84[AMR][1000 genomes]
rs9367210	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885861	chr6:44837356-45043618	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1024370	chr6:44878053-45251451	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	esv2758051	chr6:44879791-45056758	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv2759423	chr6:44879791-45056758	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv885862	chr6:44890760-45083966	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv885863	chr6:44890760-45083966	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv885864	chr6:44890760-45198796	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1023018	chr6:44925393-45152912	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv538212	chr6:44925393-45152912	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv603008	chr6:44958372-45081821	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv2762589	chr6:44982992-45044580	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1018962	chr6:44996714-45038038	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1024404	chr6:44996714-45039419	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv1026728	chr6:45001948-45126730	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv538213	chr6:45001948-45126730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv885865	chr6:45012223-45102025	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	nsv492309	chr6:45020402-45233484	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11961316	SUPT3H	cis	Frontal Cortex	GTEx
rs11961316	SUPT3H	cis	cerebellar cortex	BrainEAC

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45023400-45039200	Weak transcription	Dnd41	blood
2	chr6:45024400-45030200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:45025800-45029800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr6:45026400-45030200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:45029400-45029800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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