Variant report

Variant	rs4254936
Chromosome Location	chr5:90352452-90352453
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90351912..90354794-chr5:90458121..90460475,2	MCF-7	breast:
2	chr5:90338666..90340278-chr5:90352277..90353965,2	MCF-7	breast:
3	chr5:90333269..90336003-chr5:90350864..90353414,2	K562	blood:
4	chr5:90352115..90355751-chr5:90674816..90678609,4	MCF-7	breast:
5	chr5:90349608..90351637-chr5:90352105..90354581,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10942624	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12186662	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13179479	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13180409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1819073	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1819074	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1828177	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs1828178	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs1848486	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1848487	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1852734	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1858070	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2048217	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs2367186	0.94[ASN][1000 genomes]
rs2367274	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2463775	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2662278	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662279	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2662280	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2662281	0.88[ASN][1000 genomes]
rs2662282	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2662283	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2662284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697544	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697546	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28875340	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4454077	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452935	0.86[AMR][1000 genomes]
rs6865615	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6882081	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs689544	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7706034	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7719311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7723511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733230	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs937920	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs998788	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[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	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90341200-90376600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr5:90344400-90353800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:90344800-90368000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr5:90349400-90354000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:90349600-90354000	Weak transcription	Fetal Intestine Large	intestine
6	chr5:90349600-90354000	Weak transcription	A549	lung
7	chr5:90349600-90358400	Weak transcription	Fetal Kidney	kidney
8	chr5:90349800-90353800	Weak transcription	Colon Smooth Muscle	Colon
9	chr5:90349800-90354000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:90349800-90354200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr5:90350000-90354000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:90350600-90354600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:90350800-90354000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr5:90351000-90353800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr5:90351200-90354000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:90351600-90352800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:90351600-90353400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr5:90352400-90352600	Enhancers	Aorta	Aorta
19	chr5:90352400-90352600	Enhancers	Lung	lung
20	chr5:90352400-90367000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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