Variant report

Variant	rs9866561
Chromosome Location	chr3:105085398-105085399
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	POLR2A	chr3:105085026-105088883	GM12892	blood:	n/a	n/a
2	TEAD4	chr3:105085067-105085877	ECC-1	luminal epithelium:	n/a	n/a
3	ATF3	chr3:105085204-105085837	A549	lung:	n/a	n/a
4	NFIC	chr3:105085243-105085879	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr3:105085188-105086292	Hela-S3	cervix:	n/a	n/a
6	JUND	chr3:105084988-105085903	A549	lung:	n/a	chr3:105085314-105085322 chr3:105085486-105085495 chr3:105085313-105085323 chr3:105085312-105085324 chr3:105085313-105085323
7	E2F4	chr3:105085382-105085589	GM12878	blood:	n/a	n/a
8	ELF1	chr3:105085007-105086714	GM12878	blood:	n/a	n/a
9	EP300	chr3:105085154-105085817	SK-N-SH_RA	brain:	n/a	chr3:105085170-105085179 chr3:105085499-105085515
10	FOS	chr3:105084803-105085638	MCF10A-Er-Src	breast:	n/a	chr3:105085314-105085322 chr3:105085312-105085323 chr3:105085486-105085495 chr3:105085313-105085323 chr3:105085312-105085324 chr3:105085313-105085323
11	STAT1	chr3:105085396-105085983	GM12878	blood:	n/a	n/a
12	CBX3	chr3:105084925-105086039	HCT-116	colon:	n/a	n/a
13	USF1	chr3:105085336-105085718	H1-hESC	embryonic stem cell:	n/a	chr3:105085461-105085477
14	SIN3AK20	chr3:105084834-105086152	MCF-7	breast:	n/a	n/a
15	SP1	chr3:105085289-105085815	GM12878	blood:	n/a	chr3:105085504-105085518 chr3:105085508-105085517 chr3:105085507-105085519 chr3:105085477-105085498 chr3:105085509-105085518 chr3:105085507-105085519
16	NR3C1	chr3:105084962-105085849	A549	lung:	n/a	n/a
17	RAD21	chr3:105085168-105085901	MCF-7	breast:	n/a	chr3:105085505-105085515
18	MAX	chr3:105085177-105086904	Hela-S3	cervix:	n/a	chr3:105085313-105085322 chr3:105086357-105086366 chr3:105085558-105085565
19	BHLHE40	chr3:105085275-105086170	GM12878	blood:	n/a	chr3:105085461-105085477
20	USF1	chr3:105085279-105085801	A549	lung:	n/a	chr3:105085461-105085477
21	PBX3	chr3:105084919-105085944	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr3:105085003-105086355	HEK293	kidney:	n/a	n/a
23	USF1	chr3:105085009-105085464	A549	lung:	n/a	n/a
24	POLR2A	chr3:105085303-105085892	HepG2	liver:	n/a	n/a
25	POLR2A	chr3:105084812-105086180	HCT-116	colon:	n/a	n/a
26	JUND	chr3:105085234-105085751	HepG2	liver:	n/a	chr3:105085314-105085322 chr3:105085486-105085495 chr3:105085313-105085323 chr3:105085312-105085324 chr3:105085313-105085323
27	MAFK	chr3:105085320-105085924	Hela-S3	cervix:	n/a	n/a
28	SIN3AK20	chr3:105084561-105086326	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr3:105084872-105086371	Gliobla	brain:	n/a	n/a
30	TBP	chr3:105085371-105085805	GM12878	blood:	n/a	n/a
31	POLR2A	chr3:105085354-105088882	NB4	blood:	n/a	n/a
32	YY1	chr3:105085084-105085783	SK-N-SH_RA	brain:	n/a	chr3:105085243-105085254 chr3:105085505-105085519
33	POLR2A	chr3:105085127-105088862	GM18526	blood:	n/a	n/a
34	POLR2A	chr3:105085112-105088857	Raji	blood:	n/a	n/a
35	POLR2A	chr3:105085099-105088820	GM12892	blood:	n/a	n/a
36	GATA3	chr3:105084629-105086038	A549	lung:	n/a	chr3:105085402-105085412 chr3:105085186-105085196 chr3:105085312-105085321
37	CHD2	chr3:105084939-105086257	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr3:105084905-105086791	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr3:105085074-105085456	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr3:105085346-105087180	HL-60	blood:	n/a	n/a
41	BACH1	chr3:105084763-105086335	H1-hESC	embryonic stem cell:	n/a	n/a
42	SP4	chr3:105085376-105085796	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr3:105084967-105085923	A549	lung:	n/a	n/a
44	CTCF	chr3:105085325-105085802	MCF-7	breast:	n/a	n/a
45	USF1	chr3:105085283-105085787	A549	lung:	n/a	chr3:105085461-105085477
46	FOSL2	chr3:105084501-105085876	A549	lung:	n/a	chr3:105085314-105085322 chr3:105085486-105085495 chr3:105085313-105085323 chr3:105085312-105085324 chr3:105085313-105085323
47	RAD21	chr3:105084450-105086202	A549	lung:	n/a	chr3:105085505-105085515
48	MYC	chr3:105084236-105085998	A549	lung:	n/a	chr3:105085313-105085322 chr3:105085558-105085565
49	MBD4	chr3:105085215-105085864	HepG2	liver:	n/a	n/a
50	MAX	chr3:105085377-105085713	K562	blood:	n/a	chr3:105085558-105085565

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:104475745..104476724-chr3:105085139..105085730,2	MCF-7	breast:
2	chr3:105085252..105085785-chr3:164924215..164925187,2	MCF-7	breast:

Variant related genes	Relation type
ALCAM	TF binding region
ENSG00000244128	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs13317379	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322961	0.81[EUR][1000 genomes]
rs17181561	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17181701	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28452673	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs751554	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288807	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9822014	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825097	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9826369	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831077	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832489	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9840990	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851399	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9854028	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859198	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876906	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877002	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877483	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882494	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105083600-105086400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:105083800-105087800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:105083800-105088800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr3:105083800-105088800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr3:105084000-105085400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:105084000-105086200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:105084000-105087600	Active TSS	H1 Cell Line	embryonic stem cell
8	chr3:105084000-105088800	Active TSS	Brain Substantia Nigra	brain
9	chr3:105084000-105089000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:105084000-105089000	Active TSS	A549	lung
11	chr3:105084000-105089600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:105084200-105085400	Flanking Active TSS	HepG2	liver
13	chr3:105084200-105085800	Active TSS	Stomach Smooth Muscle	stomach
14	chr3:105084200-105087800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:105084200-105088400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:105084200-105089000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:105084200-105089000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:105084200-105089000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:105084200-105089200	Active TSS	NHDF-Ad	bronchial
20	chr3:105084200-105089600	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr3:105084200-105089600	Active TSS	NHLF	lung
22	chr3:105084200-105090400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr3:105084400-105085400	Flanking Active TSS	Liver	Liver
24	chr3:105084400-105085400	Flanking Active TSS	Colonic Mucosa	Colon
25	chr3:105084400-105085800	Bivalent/Poised TSS	Psoas Muscle	Psoas
26	chr3:105084400-105086000	Active TSS	Pancreas	Pancrea
27	chr3:105084400-105086000	Active TSS	Right Atrium	heart
28	chr3:105084400-105086200	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr3:105084400-105086200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:105084400-105086200	Active TSS	Colon Smooth Muscle	Colon
31	chr3:105084400-105086400	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr3:105084400-105086400	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr3:105084400-105086600	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr3:105084400-105087200	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr3:105084400-105087800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:105084400-105088800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:105084400-105088800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:105084400-105088800	Active TSS	Brain Cingulate Gyrus	brain
39	chr3:105084400-105088800	Active TSS	Gastric	stomach
40	chr3:105084400-105089000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:105084400-105089000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:105084400-105089000	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr3:105084400-105089000	Active TSS	Aorta	Aorta
44	chr3:105084400-105089000	Active TSS	Brain Angular Gyrus	brain
45	chr3:105084400-105089000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:105084400-105089000	Active TSS	Ovary	ovary
47	chr3:105084400-105089400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:105084400-105089400	Active TSS	GM12878-XiMat	blood
49	chr3:105084400-105089600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:105084600-105085400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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