Variant report

Variant	rs4764341
Chromosome Location	chr12:10393228-10393229
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10390106..10391990-chr12:10392432..10394861,2	K562	blood:
2	chr12:10392959..10394973-chr12:10709982..10712933,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GABARAPL1-1	chr12:10393135-10393339	XLOC_009659

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10505759	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10743875	0.97[ASN][1000 genomes]
rs10772248	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772253	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10845081	0.82[CHB][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845099	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10845100	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11053701	0.92[EUR][1000 genomes]
rs11053709	0.99[ASN][1000 genomes]
rs11053725	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12303774	0.93[EUR][1000 genomes]
rs1600130	0.81[TSI][hapmap]
rs3898121	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3912117	0.81[TSI][hapmap]
rs4254156	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs4514515	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4764331	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7314888	0.80[TSI][hapmap]
rs765791	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7953662	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7953971	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954328	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7961687	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7962865	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7963011	0.90[EUR][1000 genomes]
rs7969181	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7975352	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7976020	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv1054811	chr12:10350587-10440005	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4764341	APOLD1	cis	parietal	SCAN
rs4764341	NOP2	cis	cerebellum	SCAN
rs4764341	CLEC4A	cis	cerebellum	SCAN
rs4764341	GRIN2B	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10376400-10395000	Weak transcription	Pancreas	Pancrea
2	chr12:10376400-10397600	Weak transcription	Aorta	Aorta
3	chr12:10377200-10394200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:10377200-10394600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:10377200-10399000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:10377800-10404400	Weak transcription	Left Ventricle	heart
7	chr12:10380200-10395800	Weak transcription	Thymus	Thymus
8	chr12:10387200-10396800	Weak transcription	Liver	Liver
9	chr12:10389200-10394400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:10390200-10393400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:10390400-10394800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr12:10392000-10395600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:10392200-10393800	Weak transcription	Fetal Lung	lung
14	chr12:10392200-10395200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:10392600-10396600	Weak transcription	Adipose Nuclei	Adipose
16	chr12:10392800-10393400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:10392800-10396000	Strong transcription	Placenta	Placenta
18	chr12:10393200-10393800	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr12:10393200-10394000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr12:10393200-10394600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr12:10393200-10394800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr12:10393200-10395200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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