Variant report

Variant	rs28407980
Chromosome Location	chr4:57003378-57003379
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11723545	0.82[ASN][1000 genomes]
rs11731420	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11736354	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2127198	0.93[ASN][1000 genomes]
rs28392731	0.82[ASN][1000 genomes]
rs28418386	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28421026	0.93[ASN][1000 genomes]
rs28433043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28463663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28603237	0.82[ASN][1000 genomes]
rs28685820	0.86[AMR][1000 genomes]
rs41335053	0.82[ASN][1000 genomes]
rs6554333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686487	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv999328	chr4:56942917-57041586	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1007114	chr4:56942917-57055381	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer 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	50 gene(s)	inside rSNPs	diseases
6	nsv1012036	chr4:56963544-57106642	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56952000-57024400	Weak transcription	Fetal Intestine Small	intestine
2	chr4:56994400-57015200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:56996000-57004000	Weak transcription	Fetal Brain Male	brain
4	chr4:56996000-57015400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:56997200-57005200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:57000800-57005200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:57000800-57005400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:57000800-57005400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:57000800-57006000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:57000800-57007600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:57001000-57004000	Weak transcription	Fetal Lung	lung
12	chr4:57001000-57005400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:57001000-57013600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:57001200-57005600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:57001200-57033600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:57001600-57014000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:57002000-57005400	Weak transcription	Fetal Brain Female	brain
18	chr4:57002000-57005600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:57002000-57013000	Weak transcription	Brain Germinal Matrix	brain
20	chr4:57002000-57013200	Weak transcription	Hela-S3	cervix
21	chr4:57002200-57004000	Weak transcription	Fetal Kidney	kidney
22	chr4:57003200-57003400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived

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