Variant report

Variant	rs1899613
Chromosome Location	chr1:239835403-239835404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10754676	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10802785	0.97[ASN][1000 genomes]
rs10802788	0.86[EUR][1000 genomes]
rs10925934	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10925939	0.82[ASN][1000 genomes]
rs10925940	0.97[ASN][1000 genomes]
rs10925941	0.97[ASN][1000 genomes]
rs10925949	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12093821	0.86[EUR][1000 genomes]
rs12409845	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16838637	0.86[EUR][1000 genomes]
rs1867263	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1867264	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1867265	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1899616	0.84[EUR][1000 genomes]
rs2083817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120241	0.97[ASN][1000 genomes]
rs2165872	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4659548	0.97[ASN][1000 genomes]
rs4659550	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6429147	0.92[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6655993	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6661345	0.83[EUR][1000 genomes]
rs6665133	0.97[ASN][1000 genomes]
rs6672022	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6693851	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6700643	0.97[ASN][1000 genomes]
rs6702482	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs714803	0.91[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7551001	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv3377526	chr1:239623743-240111639	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv873351	chr1:239636613-240324200	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2757778	chr1:239766094-240389504	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv2759009	chr1:239766094-240389504	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239827800-239836800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:239832600-239839400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:239832600-239839400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:239832600-239839600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:239832600-239839800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:239833000-239840200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:239833200-239838400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:239834600-239836000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:239834600-239836400	Strong transcription	Primary hematopoietic stem cells	blood
10	chr1:239834600-239837400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:239834800-239835600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:239835200-239836000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:239835400-239835600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:239835400-239835600	Enhancers	Gastric	stomach
15	chr1:239835400-239835600	Strong transcription	Pancreas	Pancrea
16	chr1:239835400-239835800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:239835400-239835800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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