Variant report

Variant	rs12900001
Chromosome Location	chr15:49674563-49674564
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10519230	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11070693	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11631040	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11631687	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636671	0.91[ASN][1000 genomes]
rs11636795	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638378	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11638693	1.00[ASW][hapmap]
rs11852524	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap]
rs12439479	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12440534	1.00[CHB][hapmap]
rs12442701	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12913745	0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16962243	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16962490	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1904317	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap]
rs2413938	0.83[AMR][1000 genomes]
rs2413942	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs3105865	1.00[CHB][hapmap];0.93[CHD][hapmap]
rs35715933	0.83[AMR][1000 genomes]
rs4316697	0.85[GIH][hapmap]
rs4775803	1.00[CHB][hapmap]
rs520949	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs586758	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs641077	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs6493364	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs6493369	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8032650	1.00[CHB][hapmap];0.93[CHD][hapmap]
rs8041781	1.00[CHB][hapmap]
rs9920772	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv442375	chr15:49652524-49684082	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12900001	DTWD1	cis	cerebellum	SCAN
rs12900001	B2M	cis	cerebellum	SCAN
rs12900001	CATSPER2P1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49670800-49675400	Weak transcription	NHLF	lung
2	chr15:49672600-49674600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr15:49673400-49674800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr15:49673400-49675400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:49673400-49675400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:49673400-49676000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:49673400-49676200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:49673600-49674800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr15:49673600-49675400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:49673600-49676000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:49673600-49676200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr15:49673800-49683400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr15:49674000-49675000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:49674400-49677400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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