Variant report

Variant	rs7677089
Chromosome Location	chr4:88296833-88296834
allele	C/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	CTCF	chr4:88296805-88297224	HepG2	liver:	n/a	chr4:88297028-88297049 chr4:88297026-88297044
2	RAD21	chr4:88296818-88297288	HCT-116	colon:	n/a	chr4:88297027-88297046
3	NFIC	chr4:88296804-88297373	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr4:88296681-88297413	SK-N-SH	brain:	n/a	chr4:88297028-88297049 chr4:88297026-88297044
5	FOXA1	chr4:88296748-88297239	HepG2	liver:	n/a	chr4:88296993-88297005
6	RAD21	chr4:88296808-88297314	A549	lung:	n/a	chr4:88297027-88297046
7	CTCF	chr4:88296758-88297220	A549	lung:	n/a	chr4:88297028-88297049 chr4:88297026-88297044
8	CTCF	chr4:88296380-88297458	A549	lung:	n/a	chr4:88297028-88297049 chr4:88297026-88297044
9	RAD21	chr4:88296829-88297232	H1-hESC	embryonic stem cell:	n/a	chr4:88297027-88297046
10	CTCF	chr4:88296803-88297281	HCT-116	colon:	n/a	chr4:88297028-88297049 chr4:88297026-88297044
11	HNF4G	chr4:88296824-88297328	HepG2	liver:	n/a	n/a
12	RAD21	chr4:88296661-88297482	SK-N-SH	brain:	n/a	chr4:88297027-88297046
13	SMC3	chr4:88296657-88297440	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr4:88296813-88297222	MCF-7	breast:	n/a	chr4:88297028-88297049 chr4:88297026-88297044
15	RAD21	chr4:88296813-88297343	ECC-1	luminal epithelium:	n/a	chr4:88297027-88297046
16	MYBL2	chr4:88296814-88297337	HepG2	liver:	n/a	n/a
17	RAD21	chr4:88296812-88297323	HepG2	liver:	n/a	chr4:88297027-88297046
18	POLR2A	chr4:88296656-88296865	HepG2	liver:	n/a	n/a
19	RAD21	chr4:88296808-88297368	MCF-7	breast:	n/a	chr4:88297027-88297046

No.	Distal block	Cell Line	Cell type
1	chr4:88294120..88296895-chr4:88310582..88312667,2	K562	blood:
2	chr4:88293477..88300868-chr4:88308814..88313684,7	K562	blood:
3	chr4:88296681..88297512-chr4:88386982..88387860,3	MCF-7	breast:

Variant related genes	Relation type
HSD17B11	TF binding region
ENSG00000198189	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs61455435	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7665178	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7677323	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7684816	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7690005	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7696417	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88254800-88311800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:88256200-88310600	Weak transcription	Right Ventricle	heart
3	chr4:88257800-88311800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:88267400-88308000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr4:88267800-88306000	Weak transcription	Fetal Brain Female	brain
6	chr4:88271200-88298000	Weak transcription	HSMMtube	muscle
7	chr4:88273400-88298800	Weak transcription	Fetal Heart	heart
8	chr4:88274400-88297000	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr4:88274400-88303400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr4:88274600-88297200	Strong transcription	Fetal Intestine Large	intestine
11	chr4:88274800-88298200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:88275200-88299400	Strong transcription	Dnd41	blood
13	chr4:88276200-88311400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:88276400-88302800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:88278800-88297200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:88279800-88297200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr4:88282600-88303200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:88285200-88298000	Weak transcription	NH-A	brain
19	chr4:88286800-88297000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:88287400-88308000	Weak transcription	Spleen	Spleen
21	chr4:88287600-88297400	Strong transcription	Primary B cells from cord blood	blood
22	chr4:88288000-88299400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:88288600-88297200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:88289400-88297200	Strong transcription	Fetal Intestine Small	intestine
25	chr4:88289800-88297000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:88290400-88305600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr4:88290800-88301800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:88291000-88306000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:88291000-88309000	Weak transcription	Right Atrium	heart
30	chr4:88292400-88297400	Strong transcription	K562	blood
31	chr4:88293000-88304800	Weak transcription	Brain Germinal Matrix	brain
32	chr4:88293000-88306800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:88293000-88307200	Weak transcription	Pancreas	Pancrea
34	chr4:88293000-88307600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr4:88293000-88308000	Weak transcription	Colonic Mucosa	Colon
36	chr4:88293000-88308800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:88293000-88309600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:88293000-88311200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:88293200-88297000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr4:88293200-88297000	Weak transcription	Brain Substantia Nigra	brain
41	chr4:88293200-88302000	Weak transcription	Ovary	ovary
42	chr4:88293200-88308000	Weak transcription	Left Ventricle	heart
43	chr4:88293200-88309600	Weak transcription	Brain Hippocampus Middle	brain
44	chr4:88293200-88309600	Weak transcription	Gastric	stomach
45	chr4:88293200-88311400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr4:88293400-88304800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:88293400-88308000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:88293400-88309800	Weak transcription	Brain Anterior Caudate	brain
49	chr4:88293800-88297200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr4:88294000-88297000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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