Variant report

Variant	rs4102739
Chromosome Location	chr12:10480508-10480509
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10505759	0.88[CEU][hapmap]
rs10772258	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845106	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11053722	0.92[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs11053725	0.92[CEU][hapmap]
rs11608254	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11612335	0.87[EUR][1000 genomes]
rs12303914	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311695	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs12813197	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2537765	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2617135	0.92[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2617137	0.92[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2927558	0.82[ASN][1000 genomes]
rs4763505	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4764341	0.88[CEU][hapmap]
rs4764369	0.92[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs765791	0.86[CEU][hapmap]
rs7958472	0.92[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs7961687	0.88[CEU][hapmap]
rs7969664	0.82[ASN][1000 genomes]
rs7972782	0.88[CEU][hapmap]
rs7975352	0.83[CEU][hapmap]
rs7976020	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832328	chr12:10398071-10620443	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv605	chr12:10448638-10494208	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv898759	chr12:10454556-10583365	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	esv3432683	chr12:10470734-10527581	Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv3351751	chr12:10472734-10522269	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4102739	CLEC4A	cis	cerebellum	SCAN
rs4102739	APOLD1	cis	parietal	SCAN
rs4102739	NOP2	cis	cerebellum	SCAN
rs4102739	GRIN2B	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10476800-10482600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr12:10478400-10483800	Weak transcription	Right Ventricle	heart
3	chr12:10480400-10488800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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