Variant report

Variant	rs12642404
Chromosome Location	chr4:90943038-90943039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10516857	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516858	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];0.96[ASN][1000 genomes]
rs10516860	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10516862	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1117840	0.83[EUR][1000 genomes]
rs1117841	0.84[EUR][1000 genomes]
rs11732065	0.88[CEU][hapmap]
rs11933698	0.84[EUR][1000 genomes]
rs11939062	0.84[EUR][1000 genomes]
rs11939159	0.83[EUR][1000 genomes]
rs11941275	0.84[EUR][1000 genomes]
rs12500465	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12639636	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12642395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643741	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12647171	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12647266	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12648872	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12649987	0.96[EUR][1000 genomes]
rs12650363	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12651123	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13106409	0.88[EUR][1000 genomes]
rs13107286	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13108338	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13113863	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13119778	0.88[EUR][1000 genomes]
rs13120745	0.88[EUR][1000 genomes]
rs13121853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124133	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13126339	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13131070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13131903	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13132515	0.81[EUR][1000 genomes]
rs13132730	0.88[EUR][1000 genomes]
rs13143093	0.84[EUR][1000 genomes]
rs13148977	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13149395	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13150124	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13151441	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1318558	0.83[EUR][1000 genomes]
rs1443796	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1443798	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443799	0.84[EUR][1000 genomes]
rs1479430	0.83[EUR][1000 genomes]
rs1562034	0.88[EUR][1000 genomes]
rs17195014	0.83[EUR][1000 genomes]
rs17204072	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17205805	0.87[CEU][hapmap]
rs17808648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17808829	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1835521	0.87[CEU][hapmap]
rs1982293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2120372	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2120375	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34001515	0.88[EUR][1000 genomes]
rs34064092	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34343229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34886505	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34997679	0.80[EUR][1000 genomes]
rs35197902	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35817029	0.83[EUR][1000 genomes]
rs3822098	0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs55663876	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55686873	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62312682	0.82[EUR][1000 genomes]
rs62312690	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62312738	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62312743	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62313888	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6532212	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6532213	0.88[EUR][1000 genomes]
rs6814978	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6819755	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6830014	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6837222	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6854896	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs723992	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7438673	0.88[EUR][1000 genomes]
rs7660182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7661577	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677884	0.88[EUR][1000 genomes]
rs7677966	0.88[EUR][1000 genomes]
rs7685355	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs920805	0.82[EUR][1000 genomes]
rs992612	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv830005	chr4:90799398-90963420	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1003903	chr4:90831805-90947922	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1011876	chr4:90851535-90952723	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv998230	chr4:90854555-90952723	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv999030	chr4:90859531-90952723	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv432616	chr4:90862943-90952424	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv516189	chr4:90866819-90952424	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv594821	chr4:90871561-90962886	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv470053	chr4:90879613-91439573	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv879537	chr4:90883047-91165346	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90943000-90943200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:90943000-90943400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
3	chr4:90943000-90943400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr4:90943000-90943400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr4:90943000-90943600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:90943000-90943600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:90943000-90945000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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