Variant report

Variant	rs1233988
Chromosome Location	chr12:42375964-42375965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1009723	0.92[EUR][1000 genomes]
rs1016659	0.92[EUR][1000 genomes]
rs1024700	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10431604	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10748323	0.99[EUR][1000 genomes]
rs10785320	0.84[EUR][1000 genomes]
rs1226303	0.90[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs1233992	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233994	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1233996	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1234032	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1234033	0.85[EUR][1000 genomes]
rs1234034	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1234035	0.85[EUR][1000 genomes]
rs1234037	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1234038	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1234040	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1234052	0.90[EUR][1000 genomes]
rs1234054	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12826710	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1463613	0.86[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs1628871	0.83[CEU][hapmap];0.92[JPT][hapmap]
rs1688874	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1732350	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1732351	0.90[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1732352	0.86[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1882139	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1994284	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2012636	0.84[EUR][1000 genomes]
rs6582378	0.90[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs712106	0.86[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap]
rs7136038	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7303028	0.90[CEU][hapmap]
rs7305763	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7957081	0.92[EUR][1000 genomes]
rs7958455	0.94[EUR][1000 genomes]
rs7958582	0.96[EUR][1000 genomes]
rs7970115	0.87[JPT][hapmap]
rs824699	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs824716	0.86[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs824717	0.80[AMR][1000 genomes]
rs824718	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs824724	0.86[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs824734	0.90[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs824738	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs824741	0.81[JPT][hapmap]
rs844046	0.86[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap]
rs865420	0.90[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs917666	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers 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
2	nsv832387	chr12:42345541-42465505	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42362400-42376000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:42373400-42376200	Enhancers	Fetal Stomach	stomach
3	chr12:42374000-42376400	Enhancers	A549	lung
4	chr12:42374200-42376200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:42374800-42376600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr12:42375000-42378400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr12:42375200-42376000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:42375200-42376000	Weak transcription	Fetal Kidney	kidney
9	chr12:42375400-42376000	Enhancers	NHEK	skin
10	chr12:42375400-42377600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr12:42375400-42377800	Enhancers	Hela-S3	cervix
12	chr12:42375600-42376000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:42375600-42376400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:42375600-42377200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:42375800-42376000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr12:42375800-42376000	Enhancers	Brain Germinal Matrix	brain
17	chr12:42375800-42377200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:42375800-42377200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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