Variant report

Variant	rs28707598
Chromosome Location	chr4:129751857-129751858
allele	C/G
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	RUNX3	chr4:129751833-129752478	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:129751812-129753954	GM12891	blood:	n/a	n/a
3	POLR2A	chr4:129751847-129752654	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr4:129751584-129753214	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
JADE1	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10006958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10008441	0.85[AFR][1000 genomes]
rs10015538	0.88[AFR][1000 genomes]
rs10026447	0.88[AFR][1000 genomes]
rs28430630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28434631	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28583676	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28624232	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9307610	0.88[AFR][1000 genomes]
rs9991702	0.88[AFR][1000 genomes]
rs9996611	0.88[AFR][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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129734400-129756400	Weak transcription	Aorta	Aorta
2	chr4:129735400-129752200	Weak transcription	Fetal Brain Female	brain
3	chr4:129741800-129752000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:129746600-129752000	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr4:129746600-129752800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:129746600-129761800	Strong transcription	Dnd41	blood
7	chr4:129746800-129757000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:129746800-129770200	Weak transcription	HMEC	breast
9	chr4:129747000-129752000	Weak transcription	Fetal Brain Male	brain
10	chr4:129747000-129752200	Weak transcription	Hela-S3	cervix
11	chr4:129747000-129766600	Weak transcription	NHEK	skin
12	chr4:129747200-129752000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr4:129747400-129752000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:129747400-129752000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:129747400-129752000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:129747400-129752000	Weak transcription	NH-A	brain
17	chr4:129747400-129752200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:129747400-129752200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr4:129747400-129752400	Weak transcription	HSMMtube	muscle
20	chr4:129747400-129754200	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr4:129747400-129756600	Weak transcription	Esophagus	oesophagus
22	chr4:129747400-129761600	Weak transcription	Placenta	Placenta
23	chr4:129747600-129752000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:129747600-129752000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:129748000-129761600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr4:129748200-129752000	Weak transcription	Brain Angular Gyrus	brain
27	chr4:129748400-129752000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:129748600-129752000	Weak transcription	Primary B cells from cord blood	blood
29	chr4:129748600-129752000	Weak transcription	Brain Substantia Nigra	brain
30	chr4:129748800-129752000	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:129749000-129754200	Genic enhancers	H1 Cell Line	embryonic stem cell
32	chr4:129749200-129752000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:129749200-129752000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:129749600-129752000	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr4:129749600-129752000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:129749600-129752000	Weak transcription	Fetal Lung	lung
37	chr4:129749600-129752400	Enhancers	H9 Cell Line	embryonic stem cell
38	chr4:129749600-129752400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr4:129750000-129753200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr4:129750200-129752000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:129750400-129752000	Weak transcription	Fetal Muscle Leg	muscle
42	chr4:129750800-129752000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr4:129751000-129752400	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr4:129751200-129752000	Weak transcription	Fetal Thymus	thymus
45	chr4:129751400-129752000	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr4:129751400-129752000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:129751400-129752200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:129751400-129752600	Enhancers	Primary T cells fromperipheralblood	blood
49	chr4:129751400-129752600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr4:129751400-129752800	Enhancers	Lung	lung

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