Variant report

Variant	rs289693
Chromosome Location	chr1:76556101-76556102
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12408886	1.00[JPT][hapmap]
rs12408918	1.00[JPT][hapmap]
rs158620	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs158621	0.81[YRI][hapmap]
rs17098119	1.00[JPT][hapmap]
rs190861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2631779	1.00[JPT][hapmap]
rs289674	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289677	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289678	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289687	1.00[JPT][hapmap]
rs289692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs291059	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35802431	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs384233	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs403449	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs409245	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs447383	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs491409	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs551954	0.92[EUR][1000 genomes]
rs552890	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs588073	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs61558985	0.88[EUR][1000 genomes]
rs6673424	1.00[JPT][hapmap]

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	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv871862	chr1:76525783-76598209	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76542800-76572000	Weak transcription	Primary B cells from cord blood	blood
2	chr1:76545600-76558200	Weak transcription	Left Ventricle	heart
3	chr1:76548000-76561800	Weak transcription	Fetal Brain Female	brain
4	chr1:76548400-76576200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:76549000-76556200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:76549000-76556400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:76549200-76556600	Weak transcription	Brain Anterior Caudate	brain
8	chr1:76549200-76556800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:76550000-76556600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:76550200-76556800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:76551200-76556200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:76552600-76556400	Weak transcription	Brain Substantia Nigra	brain
13	chr1:76553000-76556400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:76553000-76556400	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:76553800-76556200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:76553800-76559000	Weak transcription	Fetal Kidney	kidney
17	chr1:76554000-76558600	Weak transcription	Fetal Lung	lung
18	chr1:76555600-76556200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:76555600-76557400	Enhancers	Fetal Intestine Large	intestine
20	chr1:76555600-76557400	Enhancers	Fetal Intestine Small	intestine
21	chr1:76555800-76556400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr1:76555800-76557000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:76556000-76556800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:76556000-76557400	Enhancers	H1 Cell Line	embryonic stem cell
25	chr1:76556000-76557800	Enhancers	HUES6 Cell Line	embryonic stem cell

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