Variant report

Variant	rs28709762
Chromosome Location	chr4:174099149-174099150
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:174058621..174060538-chr4:174097948..174100109,2	K562	blood:
2	chr4:174091292..174097320-chr4:174098048..174101316,8	K562	blood:
3	chr4:174088223..174092682-chr4:174092972..174099857,11	MCF-7	breast:
4	chr4:174098266..174101208-chr4:174151162..174153147,2	K562	blood:

Variant related genes	Relation type
ENSG00000245213	Chromatin interaction
ENSG00000109586	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10001613	0.87[ASN][1000 genomes]
rs10011724	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10027708	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10031414	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1054496	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1054497	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11737748	0.88[EUR][1000 genomes]
rs12503939	0.83[EUR][1000 genomes]
rs12639929	0.83[EUR][1000 genomes]
rs12644699	0.86[EUR][1000 genomes]
rs13111572	0.84[EUR][1000 genomes]
rs13125240	0.84[EUR][1000 genomes]
rs13138282	0.88[EUR][1000 genomes]
rs1574314	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17322893	0.88[EUR][1000 genomes]
rs1991727	0.84[EUR][1000 genomes]
rs2078475	0.94[EUR][1000 genomes]
rs2332654	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2332669	0.84[EUR][1000 genomes]
rs28477433	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28612521	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2877748	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733477	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4377567	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4419455	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4561909	0.90[EUR][1000 genomes]
rs4643788	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4695826	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66986541	0.80[AMR][1000 genomes]
rs6814857	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6826412	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6835098	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6851632	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7671278	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7672108	0.85[EUR][1000 genomes]
rs9990666	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9997477	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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	esv1793960	chr4:174090004-174102397	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv1801469	chr4:174090004-174102397	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1799519	chr4:174090004-174173743	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv1823585	chr4:174090209-174107537	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv3444534	chr4:174099067-174099372	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174091600-174113600	Weak transcription	Esophagus	oesophagus
2	chr4:174091800-174104000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr4:174092400-174100400	Weak transcription	Hela-S3	cervix
4	chr4:174092600-174099200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr4:174092600-174099200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr4:174092600-174102400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:174092800-174099200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr4:174092800-174099400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:174092800-174100400	Weak transcription	NHEK	skin
10	chr4:174092800-174101000	Weak transcription	HSMM	muscle
11	chr4:174092800-174103200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:174092800-174103600	Weak transcription	Aorta	Aorta
13	chr4:174092800-174106000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr4:174092800-174109000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:174093000-174102200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:174093600-174102400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:174093600-174109800	Weak transcription	Gastric	stomach
18	chr4:174093800-174105000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:174094200-174102800	Weak transcription	Brain Anterior Caudate	brain
20	chr4:174095000-174109400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:174095400-174102800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr4:174095800-174102200	Weak transcription	Primary T cells from cord blood	blood
23	chr4:174096000-174100200	Weak transcription	HUVEC	blood vessel
24	chr4:174096200-174100400	Weak transcription	Fetal Intestine Large	intestine
25	chr4:174096200-174100600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:174096200-174102000	Weak transcription	Fetal Intestine Small	intestine
27	chr4:174096200-174103200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:174096200-174111200	Weak transcription	Small Intestine	intestine
29	chr4:174096400-174101800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr4:174096800-174099200	Enhancers	K562	blood
31	chr4:174096800-174102000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:174096800-174103800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:174097000-174100400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:174097600-174101000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr4:174098000-174099200	Enhancers	Primary B cells from cord blood	blood
36	chr4:174098000-174104200	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr4:174098000-174106400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:174098200-174099600	Enhancers	Primary hematopoietic stem cells	blood
39	chr4:174098600-174099600	Weak transcription	A549	lung
40	chr4:174098600-174106200	Weak transcription	Fetal Thymus	thymus
41	chr4:174098800-174100400	Weak transcription	GM12878-XiMat	blood
42	chr4:174098800-174101800	Weak transcription	Stomach Mucosa	stomach
43	chr4:174098800-174103800	Weak transcription	Thymus	Thymus
44	chr4:174098800-174104600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:174098800-174108400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr4:174099000-174099600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:174099000-174100400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:174099000-174101800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr4:174099000-174102000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr4:174099000-174106200	Weak transcription	Dnd41	blood

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