Variant report

Variant	rs1540369
Chromosome Location	chr2:206150152-206150153
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 129 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10199654	0.91[ASN][1000 genomes]
rs10205892	0.81[ASN][1000 genomes]
rs10490290	0.80[ASN][1000 genomes]
rs10490292	0.80[ASN][1000 genomes]
rs10490293	0.80[ASN][1000 genomes]
rs10490295	0.89[ASN][1000 genomes]
rs10804147	0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs10932102	0.92[ASN][1000 genomes]
rs10932104	0.84[ASN][1000 genomes]
rs10932105	0.82[ASN][1000 genomes]
rs10932106	0.82[ASN][1000 genomes]
rs10932107	0.80[ASN][1000 genomes]
rs10932108	0.80[ASN][1000 genomes]
rs1113314	0.92[ASN][1000 genomes]
rs11676518	0.80[ASN][1000 genomes]
rs11676519	0.80[ASN][1000 genomes]
rs11676529	0.80[ASN][1000 genomes]
rs11677457	0.84[ASN][1000 genomes]
rs11686270	0.80[ASN][1000 genomes]
rs11690439	0.90[ASN][1000 genomes]
rs11690480	0.84[ASN][1000 genomes]
rs11690561	0.84[ASN][1000 genomes]
rs11691342	0.81[ASN][1000 genomes]
rs11691345	0.82[ASN][1000 genomes]
rs11692923	0.92[ASN][1000 genomes]
rs11695465	0.84[ASN][1000 genomes]
rs1207411	0.83[ASN][1000 genomes]
rs1207415	0.84[ASN][1000 genomes]
rs1207421	0.86[ASN][1000 genomes]
rs1207424	0.81[ASN][1000 genomes]
rs1207426	0.84[ASN][1000 genomes]
rs1207428	0.84[ASN][1000 genomes]
rs1207429	0.83[ASN][1000 genomes]
rs1207430	0.84[ASN][1000 genomes]
rs1207431	0.84[ASN][1000 genomes]
rs1207432	0.84[ASN][1000 genomes]
rs1207433	0.84[ASN][1000 genomes]
rs1207440	0.84[ASN][1000 genomes]
rs1207441	0.84[ASN][1000 genomes]
rs1211319	0.80[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs12373584	0.80[ASN][1000 genomes]
rs12373610	0.80[ASN][1000 genomes]
rs12464688	0.80[ASN][1000 genomes]
rs12464755	0.92[ASN][1000 genomes]
rs12468755	0.85[ASN][1000 genomes]
rs12468794	0.85[ASN][1000 genomes]
rs12468975	0.82[ASN][1000 genomes]
rs12470003	0.80[ASN][1000 genomes]
rs12470079	0.80[ASN][1000 genomes]
rs12470434	0.85[ASN][1000 genomes]
rs12476682	0.84[ASN][1000 genomes]
rs12615597	0.92[ASN][1000 genomes]
rs12622101	0.92[ASN][1000 genomes]
rs12623757	0.84[ASN][1000 genomes]
rs12989507	0.84[ASN][1000 genomes]
rs13000324	0.80[ASN][1000 genomes]
rs13002238	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13004164	0.85[ASN][1000 genomes]
rs13004568	0.91[ASN][1000 genomes]
rs13009974	0.84[ASN][1000 genomes]
rs13011880	0.84[ASN][1000 genomes]
rs13011981	0.84[ASN][1000 genomes]
rs13022810	0.91[ASN][1000 genomes]
rs1398053	0.80[ASN][1000 genomes]
rs1398054	0.80[ASN][1000 genomes]
rs1511873	0.84[ASN][1000 genomes]
rs1511874	0.84[ASN][1000 genomes]
rs1540365	0.92[ASN][1000 genomes]
rs1540366	0.92[ASN][1000 genomes]
rs1540367	0.93[ASN][1000 genomes]
rs1540368	0.93[ASN][1000 genomes]
rs1606238	0.84[ASN][1000 genomes]
rs1606239	0.84[ASN][1000 genomes]
rs17201041	0.84[ASN][1000 genomes]
rs1861508	0.92[ASN][1000 genomes]
rs1861509	0.92[ASN][1000 genomes]
rs1861514	0.84[ASN][1000 genomes]
rs1877338	0.80[ASN][1000 genomes]
rs1877339	0.80[ASN][1000 genomes]
rs1912845	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1921805	0.92[ASN][1000 genomes]
rs2041877	0.82[ASN][1000 genomes]
rs2080418	0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2080419	0.84[ASN][1000 genomes]
rs2160455	0.85[ASN][1000 genomes]
rs2251539	0.84[ASN][1000 genomes]
rs2336416	0.92[ASN][1000 genomes]
rs2336417	0.86[ASN][1000 genomes]
rs2336420	0.80[ASN][1000 genomes]
rs2541149	0.82[ASN][1000 genomes]
rs2704643	0.84[ASN][1000 genomes]
rs2878692	0.84[ASN][1000 genomes]
rs34226321	0.93[ASN][1000 genomes]
rs34486316	0.80[ASN][1000 genomes]
rs35337631	0.80[ASN][1000 genomes]
rs3843339	0.85[ASN][1000 genomes]
rs3845806	0.85[ASN][1000 genomes]
rs3856509	0.92[ASN][1000 genomes]
rs3928642	0.85[ASN][1000 genomes]
rs4119079	0.92[ASN][1000 genomes]
rs4119081	0.92[ASN][1000 genomes]
rs4505506	0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs4673318	0.92[ASN][1000 genomes]
rs4673319	0.85[ASN][1000 genomes]
rs4673320	0.84[ASN][1000 genomes]
rs4673323	0.82[ASN][1000 genomes]
rs4673324	0.82[ASN][1000 genomes]
rs4673326	0.80[ASN][1000 genomes]
rs4673327	0.80[ASN][1000 genomes]
rs4673328	0.80[ASN][1000 genomes]
rs4675508	0.90[ASN][1000 genomes]
rs4675511	0.92[ASN][1000 genomes]
rs4675513	0.92[ASN][1000 genomes]
rs4675515	0.85[ASN][1000 genomes]
rs4675519	0.84[ASN][1000 genomes]
rs55850246	0.92[ASN][1000 genomes]
rs62171506	0.84[ASN][1000 genomes]
rs66583439	0.80[ASN][1000 genomes]
rs6740963	0.80[ASN][1000 genomes]
rs6761373	0.85[ASN][1000 genomes]
rs7582340	0.81[ASN][1000 genomes]
rs7594732	0.92[ASN][1000 genomes]
rs964896	0.80[ASN][1000 genomes]
rs964897	0.80[ASN][1000 genomes]
rs979187	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998485	chr2:205407813-206184006	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv536122	chr2:205407813-206184006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1012780	chr2:206124954-206546271	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv3340146	chr2:206149496-206150853	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1540369	CRYGC	cis	cerebellum	SCAN
rs1540369	ALS2CR12	cis	parietal	SCAN
rs1540369	PLEKHM3	cis	cerebellum	SCAN
rs1540369	PARD3B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:206097200-206170600	Weak transcription	HSMMtube	muscle
2	chr2:206118200-206156600	Weak transcription	Aorta	Aorta
3	chr2:206138800-206162200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:206149000-206156800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:206149200-206150800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:206149400-206154200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:206149400-206154600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:206149400-206158200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:206149400-206160000	Weak transcription	Psoas Muscle	Psoas
10	chr2:206149600-206154600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:206149600-206158200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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