Variant report

Variant	rs476844
Chromosome Location	chr12:10137296-10137297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1060648	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1081386	0.84[ASN][1000 genomes]
rs12298261	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1359081	0.85[ASN][1000 genomes]
rs2760953	0.81[MEX][hapmap]
rs2961544	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs3903806	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3903807	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4611291	0.85[ASN][1000 genomes]
rs4764177	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4764187	0.89[GIH][hapmap]
rs479499	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519291	0.89[AFR][1000 genomes]
rs526157	0.81[MEX][hapmap]
rs531425	0.87[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs544783	0.82[ASN][1000 genomes]
rs545677	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs566229	0.85[AFR][1000 genomes]
rs570082	0.85[AFR][1000 genomes]
rs570931	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs574097	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs576031	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs588272	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs607567	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs608418	0.87[AFR][1000 genomes]
rs609216	0.84[AFR][1000 genomes]
rs623182	0.83[AFR][1000 genomes]
rs623269	0.87[AFR][1000 genomes]
rs623728	0.87[AFR][1000 genomes]
rs632963	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs633874	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs636554	0.82[ASN][1000 genomes]
rs640817	0.81[MEX][hapmap]
rs678208	0.84[ASN][1000 genomes]
rs679982	0.84[ASN][1000 genomes]
rs684134	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960084	0.89[GIH][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	nsv898755	chr12:10069302-10186284	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1038226	chr12:10121288-10143591	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1043125	chr12:10121288-10177037	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1042106	chr12:10121288-10177636	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1040610	chr12:10121288-10179374	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv525593	chr12:10121347-10156646	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs476844	SCARNA12	cis	cerebellum	SCAN
rs476844	CLEC12A	cis	normal skin	skin_eQTL
rs476844	PRB3	cis	cerebellum	SCAN
rs476844	PRH2	cis	parietal	SCAN
rs476844	ATN1	cis	cerebellum	SCAN
rs476844	LOC653113	cis	parietal	SCAN
rs476844	GABARAPL1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10129200-10144400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:10130400-10138600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:10132400-10140800	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:10133400-10139400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr12:10133600-10140200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:10135800-10144600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:10137200-10138200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr12:10137200-10138800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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