Variant report

Variant	rs28539861
Chromosome Location	chr5:178367805-178367806
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	POLR2A	chr5:178367711-178368522	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr5:178367353-178367853	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF1	chr5:178367708-178368396	H1-hESC	embryonic stem cell:	n/a	n/a
4	E2F6	chr5:178367461-178367844	H1-hESC	embryonic stem cell:	n/a	n/a
5	MXI1	chr5:178367375-178368905	SK-N-SH	brain:	n/a	chr5:178368168-178368183
6	NRF1	chr5:178367767-178368521	SK-N-SH	brain:	n/a	chr5:178368183-178368197 chr5:178368180-178368194 chr5:178368183-178368192 chr5:178368183-178368194
7	ZNF143	chr5:178367613-178368324	H1-hESC	embryonic stem cell:	n/a	chr5:178368099-178368117
8	E2F6	chr5:178367319-178368602	H1-hESC	embryonic stem cell:	n/a	chr5:178368184-178368193
9	MAX	chr5:178367363-178368443	H1-hESC	embryonic stem cell:	n/a	chr5:178368174-178368183

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRM6-1	chr5:178366753-178368084	ENSG00000248595

Variant related genes	Relation type
ENSG00000272431	TF binding region
ZNF454	TF binding region

rs_ID	r²[population]
rs11949180	0.80[EUR][1000 genomes]
rs11949181	0.80[EUR][1000 genomes]
rs11949892	0.80[EUR][1000 genomes]
rs11958887	0.80[EUR][1000 genomes]
rs12186577	0.96[EUR][1000 genomes]
rs12186584	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12187167	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12553	0.82[EUR][1000 genomes]
rs57438229	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59849584	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61744382	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6859174	0.82[EUR][1000 genomes]
rs6861717	0.80[EUR][1000 genomes]
rs6863202	0.80[EUR][1000 genomes]
rs6863603	0.82[EUR][1000 genomes]
rs6878353	0.82[EUR][1000 genomes]
rs6894878	0.82[EUR][1000 genomes]
rs7706558	0.82[EUR][1000 genomes]
rs7731067	0.82[EUR][1000 genomes]

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178352400-178369200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:178353800-178374800	ZNF genes & repeats	Liver	Liver
3	chr5:178362800-178369000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
4	chr5:178363200-178369000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
5	chr5:178363800-178369000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:178364000-178368800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
7	chr5:178364600-178369200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr5:178365200-178369200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:178366000-178368000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
10	chr5:178366000-178370200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
11	chr5:178366200-178368000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:178366200-178368200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
13	chr5:178366400-178369000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
14	chr5:178366400-178369200	ZNF genes & repeats	Lung	lung
15	chr5:178366400-178372600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:178366600-178369000	Active TSS	Stomach Mucosa	stomach
17	chr5:178366800-178368000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
18	chr5:178366800-178368800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:178366800-178368800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
20	chr5:178366800-178368800	Active TSS	Brain Angular Gyrus	brain
21	chr5:178366800-178369000	Active TSS	Brain Cingulate Gyrus	brain
22	chr5:178366800-178369000	ZNF genes & repeats	HSMMtube	muscle
23	chr5:178366800-178370200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
24	chr5:178366800-178370200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr5:178366800-178370400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:178367000-178368600	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr5:178367000-178368800	Active TSS	Psoas Muscle	Psoas
28	chr5:178367000-178369000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
29	chr5:178367000-178369000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:178367000-178370400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
31	chr5:178367000-178374600	ZNF genes & repeats	Spleen	Spleen
32	chr5:178367200-178368000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
33	chr5:178367200-178368400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:178367200-178368400	Active TSS	Stomach Smooth Muscle	stomach
35	chr5:178367200-178368600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:178367200-178368600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:178367200-178368600	Active TSS	Fetal Intestine Small	intestine
38	chr5:178367200-178368600	Active TSS	Ovary	ovary
39	chr5:178367200-178368800	Active TSS	Colon Smooth Muscle	Colon
40	chr5:178367200-178368800	Active TSS	NHDF-Ad	bronchial
41	chr5:178367200-178368800	ZNF genes & repeats	NHEK	skin
42	chr5:178367200-178368800	Active TSS	NHLF	lung
43	chr5:178367200-178369000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:178367200-178369000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:178367200-178369000	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr5:178367200-178369000	Active TSS	Right Atrium	heart
47	chr5:178367200-178369000	ZNF genes & repeats	HSMM	muscle
48	chr5:178367200-178369000	Active TSS	Osteobl	bone
49	chr5:178367200-178369200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
50	chr5:178367400-178368000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose

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