Variant report

Variant	rs8192554
Chromosome Location	chr2:182545461-182545462
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	MAX	chr2:182545208-182545776	SK-N-SH	brain:	n/a	chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545688-182545698 chr2:182545529-182545538 chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545527-182545540 chr2:182545528-182545539 chr2:182545528-182545537
2	RAD21	chr2:182545379-182545752	SK-N-SH_RA	brain:	n/a	n/a
3	MAX	chr2:182545130-182546027	H1-hESC	embryonic stem cell:	n/a	chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545688-182545698 chr2:182545529-182545538 chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545527-182545540 chr2:182545528-182545539 chr2:182545528-182545537
4	USF1	chr2:182545446-182545713	A549	lung:	n/a	n/a
5	USF1	chr2:182545430-182545636	GM12878	blood:	n/a	n/a
6	ZNF143	chr2:182545205-182545898	H1-hESC	embryonic stem cell:	n/a	n/a
7	TEAD4	chr2:182545276-182545751	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZNF263	chr2:182545063-182545669	HEK293-T-REx	kidney:	n/a	n/a
9	REST	chr2:182545451-182545653	SK-N-SH	brain:	n/a	n/a
10	HDAC2	chr2:182545427-182545802	H1-hESC	embryonic stem cell:	n/a	chr2:182545706-182545720
11	MAX	chr2:182545085-182545735	A549	lung:	n/a	chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545688-182545698 chr2:182545529-182545538 chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545527-182545540 chr2:182545528-182545539 chr2:182545528-182545537
12	USF2	chr2:182545357-182545726	H1-hESC	embryonic stem cell:	n/a	n/a
13	CREB1	chr2:182545145-182545622	H1-hESC	embryonic stem cell:	n/a	n/a
14	MYC	chr2:182545370-182545756	H1-hESC	embryonic stem cell:	n/a	chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545688-182545698 chr2:182545529-182545538 chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545527-182545540 chr2:182545528-182545539 chr2:182545528-182545537
15	USF1	chr2:182545344-182545766	A549	lung:	n/a	n/a
16	CHD2	chr2:182545091-182546434	H1-hESC	embryonic stem cell:	n/a	chr2:182545690-182545700 chr2:182546240-182546249
17	RAD21	chr2:182545388-182545561	H1-hESC	embryonic stem cell:	n/a	n/a
18	E2F6	chr2:182545082-182546025	H1-hESC	embryonic stem cell:	n/a	chr2:182545763-182545770 chr2:182545763-182545770 chr2:182545763-182545770
19	USF1	chr2:182545358-182545718	A549	lung:	n/a	n/a
20	USF1	chr2:182545229-182545841	H1-hESC	embryonic stem cell:	n/a	n/a
21	YY1	chr2:182545440-182545767	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr2:182544920-182545565	H1-neurons	neurons:	n/a	n/a
23	USF1	chr2:182545143-182545730	SK-N-SH_RA	brain:	n/a	n/a
24	TCF12	chr2:182545438-182545763	H1-hESC	embryonic stem cell:	n/a	n/a
25	USF1	chr2:182545332-182545761	SK-N-SH_RA	brain:	n/a	n/a
26	EP300	chr2:182545244-182545634	SK-N-SH_RA	brain:	n/a	n/a
27	MAX	chr2:182545162-182546012	H1-hESC	embryonic stem cell:	n/a	chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545688-182545698 chr2:182545529-182545538 chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545527-182545540 chr2:182545528-182545539 chr2:182545528-182545537
28	SP1	chr2:182545343-182545882	H1-hESC	embryonic stem cell:	n/a	chr2:182545691-182545700 chr2:182545574-182545581 chr2:182545687-182545701 chr2:182545690-182545702
29	SUZ12	chr2:182543491-182550280	NT2-D1	testis:	n/a	n/a
30	NRF1	chr2:182544976-182545766	SK-N-SH	brain:	n/a	n/a
31	SUZ12	chr2:182545142-182546680	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr2:182545234-182545900	H1-hESC	embryonic stem cell:	n/a	chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545688-182545698 chr2:182545529-182545538 chr2:182545529-182545538 chr2:182545527-182545540 chr2:182545527-182545540 chr2:182545528-182545539 chr2:182545528-182545537
33	EP300	chr2:182545362-182545677	SK-N-SH_RA	brain:	n/a	n/a
34	TEAD4	chr2:182545333-182545713	H1-hESC	embryonic stem cell:	n/a	n/a
35	USF1	chr2:182545288-182545905	SK-N-SH	brain:	n/a	n/a
36	USF1	chr2:182545266-182545736	H1-hESC	embryonic stem cell:	n/a	n/a
37	BACH1	chr2:182545187-182545744	H1-hESC	embryonic stem cell:	n/a	n/a
38	USF1	chr2:182545402-182545779	K562	blood:	n/a	n/a
39	E2F6	chr2:182545208-182545775	H1-hESC	embryonic stem cell:	n/a	chr2:182545763-182545770 chr2:182545763-182545770 chr2:182545763-182545770
40	MXI1	chr2:182545186-182545729	H1-hESC	embryonic stem cell:	n/a	chr2:182545530-182545539
41	SIN3A	chr2:182545141-182546037	H1-hESC	embryonic stem cell:	n/a	chr2:182545530-182545539
42	USF1	chr2:182545386-182545658	A549	lung:	n/a	n/a
43	USF1	chr2:182545325-182545851	SK-N-SH	brain:	n/a	n/a
44	ATF3	chr2:182545456-182545700	H1-hESC	embryonic stem cell:	n/a	n/a
45	NRF1	chr2:182545167-182545543	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTBP2	chr2:182545133-182546496	H1-hESC	embryonic stem cell:	n/a	n/a
47	USF1	chr2:182545426-182545669	A549	lung:	n/a	n/a
48	JUND	chr2:182545317-182545788	H1-hESC	embryonic stem cell:	n/a	n/a
49	YY1	chr2:182545098-182546152	H1-hESC	embryonic stem cell:	n/a	n/a
50	SP1	chr2:182545396-182545845	H1-hESC	embryonic stem cell:	n/a	chr2:182545691-182545700 chr2:182545574-182545581 chr2:182545687-182545701 chr2:182545690-182545702

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITGA4-1	chr2:182545394-182546506	NONHSAT075881

Variant related genes	Relation type
ENSG00000234595	TF binding region
CERKL	TF binding region
NEUROD1	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10188644	0.91[EUR][1000 genomes]
rs10497584	0.91[EUR][1000 genomes]
rs12616753	0.91[EUR][1000 genomes]
rs12616809	0.91[EUR][1000 genomes]
rs12617923	0.91[EUR][1000 genomes]
rs12619962	0.91[EUR][1000 genomes]
rs12623595	0.91[EUR][1000 genomes]
rs16867481	0.91[EUR][1000 genomes]
rs16867483	0.91[EUR][1000 genomes]
rs16867485	0.91[EUR][1000 genomes]
rs16867486	0.91[EUR][1000 genomes]
rs16867487	0.91[EUR][1000 genomes]
rs16867489	0.91[EUR][1000 genomes]
rs16867490	0.91[EUR][1000 genomes]
rs16867491	0.91[EUR][1000 genomes]
rs16867492	0.91[EUR][1000 genomes]
rs2696341	0.91[EUR][1000 genomes]
rs28394061	0.91[EUR][1000 genomes]
rs28464322	0.91[EUR][1000 genomes]
rs28589860	0.91[EUR][1000 genomes]
rs28654292	0.91[EUR][1000 genomes]
rs28718983	0.91[EUR][1000 genomes]
rs58618231	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv834477	chr2:182438121-182593527	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182542400-182546200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
2	chr2:182543000-182545600	Bivalent/Poised TSS	Fetal Brain Female	brain
3	chr2:182543600-182550200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr2:182544000-182545600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
5	chr2:182544200-182545600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:182544800-182545600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:182544800-182545600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
8	chr2:182545000-182545600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
9	chr2:182545000-182545600	Bivalent/Poised TSS	A549	lung
10	chr2:182545000-182545800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:182545000-182545800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr2:182545000-182545800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr2:182545000-182545800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:182545000-182546000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr2:182545000-182546200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:182545000-182546200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:182545000-182546200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
18	chr2:182545000-182547200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
19	chr2:182545000-182548000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:182545000-182548400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
21	chr2:182545200-182545600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
22	chr2:182545200-182545600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:182545200-182545600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
24	chr2:182545200-182545600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
25	chr2:182545200-182545600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
26	chr2:182545200-182545600	Bivalent Enhancer	Fetal Intestine Small	intestine
27	chr2:182545200-182545600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr2:182545200-182545600	Bivalent Enhancer	Fetal Stomach	stomach
29	chr2:182545200-182545600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
30	chr2:182545200-182545800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
31	chr2:182545200-182545800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
32	chr2:182545200-182545800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:182545200-182545800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:182545200-182545800	Enhancers	Right Atrium	heart
35	chr2:182545200-182545800	Bivalent/Poised TSS	NHLF	lung
36	chr2:182545200-182546000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:182545200-182546000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
38	chr2:182545200-182546000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
39	chr2:182545200-182546000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
40	chr2:182545200-182546000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:182545200-182546000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:182545200-182546000	Bivalent Enhancer	Placenta	Placenta
43	chr2:182545200-182546000	Enhancers	Gastric	stomach
44	chr2:182545200-182546000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
45	chr2:182545200-182546200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:182545200-182546200	Bivalent Enhancer	Colonic Mucosa	Colon
47	chr2:182545200-182546200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
48	chr2:182545200-182546200	Bivalent Enhancer	Fetal Heart	heart
49	chr2:182545200-182546200	Bivalent Enhancer	Fetal Muscle Leg	muscle
50	chr2:182545200-182546400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast

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