Variant report

Variant	rs2028642
Chromosome Location	chr4:82075064-82075065
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr4:82074825-82075484	H1-hESC	embryonic stem cell:	n/a	n/a
2	TBP	chr4:82074693-82075297	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr4:82075025-82075464	A549	lung:	n/a	n/a
4	CEBPB	chr4:82074553-82075216	A549	lung:	n/a	chr4:82074711-82074722
5	HEY1	chr4:82074840-82075091	K562	blood:	n/a	n/a
6	POLR2A	chr4:82075057-82075183	A549	lung:	n/a	n/a
7	TAF1	chr4:82074748-82075491	H1-hESC	embryonic stem cell:	n/a	n/a
8	YY1	chr4:82074764-82075393	H1-hESC	embryonic stem cell:	n/a	chr4:82074918-82074930
9	POLR2A	chr4:82074841-82075462	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr4:82074961-82075377	A549	lung:	n/a	n/a
11	POLR2A	chr4:82074566-82075740	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr4:82074859-82075434	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr4:82074890-82075136	Hela-S3	cervix:	n/a	n/a
14	MYC	chr4:82074998-82075120	MCF-7	breast:	n/a	n/a
15	CHD2	chr4:82075038-82075273	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr4:82074895-82075134	MCF-7	breast:	n/a	n/a
17	TAF1	chr4:82074714-82075344	A549	lung:	n/a	n/a
18	POLR2A	chr4:82074790-82075095	H1-hESC	embryonic stem cell:	n/a	n/a
19	TBP	chr4:82074836-82075093	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr4:82075003-82075412	Hela-S3	cervix:	n/a	n/a
21	CEBPB	chr4:82074514-82075285	Hela-S3	cervix:	n/a	chr4:82074711-82074722
22	YY1	chr4:82074788-82075500	A549	lung:	n/a	chr4:82074918-82074930
23	FOXA2	chr4:82074989-82075760	A549	lung:	n/a	n/a
24	POLR2A	chr4:82074776-82075470	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr4:82075046-82075172	A549	lung:	n/a	n/a

Variant related genes	Relation type
PRKG2	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10003341	0.86[EUR][1000 genomes]
rs10005912	0.86[EUR][1000 genomes]
rs10516650	0.86[EUR][1000 genomes]
rs11099460	0.86[EUR][1000 genomes]
rs11722020	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11733213	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11933194	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12330930	0.86[EUR][1000 genomes]
rs12331759	0.86[EUR][1000 genomes]
rs12331821	0.86[EUR][1000 genomes]
rs12332035	0.86[EUR][1000 genomes]
rs12643702	0.86[EUR][1000 genomes]
rs12651341	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1517547	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1545287	0.86[EUR][1000 genomes]
rs1546651	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1972127	0.84[EUR][1000 genomes]
rs28419569	0.80[EUR][1000 genomes]
rs28445932	0.86[EUR][1000 genomes]
rs28491787	0.86[EUR][1000 genomes]
rs28669195	0.86[EUR][1000 genomes]
rs2868141	0.86[EUR][1000 genomes]
rs28783134	0.86[EUR][1000 genomes]
rs3733550	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3943629	0.86[EUR][1000 genomes]
rs4566647	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56008646	0.86[EUR][1000 genomes]
rs59896344	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60111302	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6828114	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6848802	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6857403	0.82[EUR][1000 genomes]
rs72878860	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72879491	0.86[EUR][1000 genomes]
rs72879493	0.86[EUR][1000 genomes]
rs72879502	0.82[EUR][1000 genomes]
rs72880604	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72881305	0.82[EUR][1000 genomes]
rs7687258	0.84[EUR][1000 genomes]
rs986290	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999729	chr4:81802554-82627820	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537156	chr4:81802554-82627820	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv829984	chr4:81979988-82113977	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	esv1822437	chr4:82025743-82118996	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:82071000-82085400	Weak transcription	NHDF-Ad	bronchial
2	chr4:82074200-82075200	Enhancers	HMEC	breast
3	chr4:82074200-82075400	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr4:82074400-82075200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:82074400-82075200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:82074400-82075400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr4:82074400-82075400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:82074400-82075400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr4:82074400-82075400	Active TSS	Rectal Smooth Muscle	rectum
10	chr4:82074400-82075800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr4:82074600-82075400	Active TSS	H1 Cell Line	embryonic stem cell
12	chr4:82074600-82075400	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr4:82074600-82075400	Active TSS	Colonic Mucosa	Colon
14	chr4:82074600-82075400	Active TSS	Fetal Intestine Large	intestine
15	chr4:82074600-82075400	Active TSS	A549	lung
16	chr4:82074600-82075400	Active TSS	Hela-S3	cervix
17	chr4:82074800-82075200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:82074800-82075400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr4:82074800-82075400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:82074800-82075400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr4:82074800-82075400	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr4:82074800-82075400	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr4:82074800-82075400	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr4:82074800-82075400	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr4:82074800-82075400	Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr4:82074800-82075400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr4:82074800-82075400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:82074800-82075400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:82074800-82075400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:82074800-82075400	Active TSS	Duodenum Mucosa	Duodenum
31	chr4:82074800-82075400	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr4:82074800-82075400	Active TSS	Esophagus	oesophagus
33	chr4:82074800-82075400	Active TSS	Fetal Intestine Small	intestine
34	chr4:82074800-82075400	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr4:82074800-82075400	Active TSS	K562	blood
36	chr4:82075000-82075200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:82075000-82075200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:82075000-82075200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:82075000-82075400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:82075000-82075400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:82075000-82075400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr4:82075000-82075400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr4:82075000-82075400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:82075000-82075400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:82075000-82075400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:82075000-82075400	Active TSS	Primary T cells fromperipheralblood	blood
47	chr4:82075000-82075400	Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr4:82075000-82075400	Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr4:82075000-82075400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr4:82075000-82075400	Active TSS	Primary T helper cells PMA-I stimulated	--

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