Variant report

Variant	rs4972379
Chromosome Location	chr2:149335544-149335545
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12615627	0.84[EUR][1000 genomes]
rs12620020	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12622366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12691800	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12691802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13014625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13014829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1550858	0.96[EUR][1000 genomes]
rs16828718	0.87[CEU][hapmap]
rs1868396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868397	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4609986	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4972284	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4972376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4972385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55933306	0.87[EUR][1000 genomes]
rs56797270	0.98[EUR][1000 genomes]
rs57835656	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6708007	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73005293	0.98[EUR][1000 genomes]
rs73005300	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73005302	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73007306	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73007314	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73007341	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73016733	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7579702	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7592968	0.87[CEU][hapmap]
rs7601936	0.87[CEU][hapmap]
rs9287418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs978509	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751831	chr2:149151358-150105603	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1000101	chr2:149165813-149361220	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv868861	chr2:149198443-149434604	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv917109	chr2:149198443-149948302	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1004663	chr2:149214090-149373061	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv2762913	chr2:149249683-149345487	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 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	chr2:149332800-149336800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:149333800-149336800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
3	chr2:149334200-149335600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
4	chr2:149334400-149336400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr2:149334600-149336600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:149334800-149335800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:149335000-149336000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:149335000-149336800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr2:149335200-149336400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr2:149335200-149337000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:149335400-149335600	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:149335400-149335800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr2:149335400-149335800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
14	chr2:149335400-149336400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr2:149335400-149336400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:149335400-149336600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr2:149335400-149336800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:149335400-149338600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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