Variant report

Variant	rs28657625
Chromosome Location	chr4:7854160-7854161
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7847678..7850223-chr4:7853513..7856293,3	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs28393652	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28418478	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28451112	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28468456	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28508479	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28612887	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28621561	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28638094	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28649910	0.86[EUR][1000 genomes]
rs28657375	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28662492	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28728216	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28861809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075363	0.85[ASN][1000 genomes]
rs4377592	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4383619	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4388087	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4404542	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413405	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4473655	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4496581	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4496582	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4552460	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4605652	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4623000	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838291	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7821200-7859000	Weak transcription	Aorta	Aorta
2	chr4:7825800-7854200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:7830400-7862600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:7830600-7855200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:7830600-7856200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:7830600-7857200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:7830600-7862200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:7830600-7862400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:7830800-7854400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:7833800-7855200	Weak transcription	Spleen	Spleen
11	chr4:7836600-7855200	Weak transcription	Fetal Kidney	kidney
12	chr4:7843600-7863000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:7845000-7856400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:7845000-7858600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:7845000-7863200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:7845200-7859000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:7846200-7860200	Weak transcription	Small Intestine	intestine
18	chr4:7846400-7857200	Weak transcription	Left Ventricle	heart
19	chr4:7846600-7854200	Weak transcription	Brain Substantia Nigra	brain
20	chr4:7846800-7858400	Weak transcription	Fetal Heart	heart
21	chr4:7847200-7854400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:7847600-7858400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:7847800-7855600	Strong transcription	HSMMtube	muscle
24	chr4:7848000-7857000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:7848000-7857400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr4:7848000-7857400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr4:7848000-7872200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr4:7848200-7854600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr4:7848200-7862000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr4:7848400-7858200	Weak transcription	Fetal Brain Male	brain
31	chr4:7848600-7856800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:7849200-7854400	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr4:7849200-7857000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:7849400-7857600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:7849600-7854800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:7850000-7857800	Strong transcription	Fetal Intestine Small	intestine
37	chr4:7850200-7857000	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr4:7850400-7854400	Strong transcription	Brain Germinal Matrix	brain
39	chr4:7850400-7857800	Strong transcription	Fetal Intestine Large	intestine
40	chr4:7850400-7858400	Weak transcription	Right Ventricle	heart
41	chr4:7850600-7854600	Strong transcription	NHEK	skin
42	chr4:7850600-7857400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:7850800-7856000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr4:7850800-7857000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
45	chr4:7850800-7857400	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr4:7851000-7855000	Genic enhancers	A549	lung
47	chr4:7851200-7854200	Strong transcription	Fetal Lung	lung
48	chr4:7851200-7857400	Strong transcription	NHLF	lung
49	chr4:7851400-7857400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr4:7851600-7856000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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