Variant report

Variant	rs9309462
Chromosome Location	chr2:72372986-72372987
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	SP1	chr2:72371739-72373077	A549	lung:	n/a	chr2:72371991-72372003 chr2:72371883-72371892 chr2:72371881-72371893 chr2:72372832-72372846 chr2:72371988-72372002 chr2:72372832-72372842 chr2:72372654-72372665 chr2:72372242-72372254 chr2:72371991-72372003 chr2:72372145-72372154 chr2:72371987-72371996 chr2:72372239-72372253 chr2:72371986-72371998 chr2:72372831-72372843 chr2:72372539-72372553 chr2:72372144-72372156 chr2:72372243-72372252 chr2:72371988-72371997 chr2:72372146-72372155 chr2:72372144-72372155 chr2:72372244-72372253 chr2:72372542-72372554 chr2:72371988-72371997 chr2:72371986-72371998 chr2:72372831-72372843 chr2:72372833-72372842 chr2:72372144-72372156 chr2:72372242-72372254 chr2:72371881-72371893 chr2:72372826-72372840 chr2:72372194-72372204 chr2:72372582-72372593 chr2:72372579-72372593 chr2:72371993-72372002
2	SMC3	chr2:72371868-72372998	Hela-S3	cervix:	n/a	chr2:72372536-72372546
3	POLR2A	chr2:72371849-72375638	SK-N-MC	brain:	n/a	n/a
4	TCF12	chr2:72371615-72374467	A549	lung:	n/a	chr2:72373796-72373806
5	E2F6	chr2:72371677-72373007	A549	lung:	n/a	n/a
6	MAX	chr2:72371598-72378199	A549	lung:	n/a	chr2:72377135-72377144 chr2:72372838-72372848 chr2:72372537-72372547 chr2:72374470-72374480 chr2:72375058-72375068 chr2:72376080-72376090 chr2:72374306-72374316
7	TCF7L2	chr2:72371853-72373215	Hela-S3	cervix:	n/a	n/a
8	RCOR1	chr2:72371541-72373258	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr2:72370915-72373823	Hela-S3	cervix:	n/a	n/a
10	SUZ12	chr2:72372948-72375201	NT2-D1	testis:	n/a	n/a
11	REST	chr2:72371802-72373136	A549	lung:	n/a	chr2:72372228-72372238 chr2:72372129-72372138 chr2:72372221-72372234
12	CTBP2	chr2:72371710-72375657	H1-hESC	embryonic stem cell:	n/a	n/a
13	HA-E2F1	chr2:72371773-72373204	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:72372965-72373015	ProgFib	skin:	n/a
2	chr2:72372965-72373015	SK-N-SH_RA	brain:	n/a
3	chr2:72372965-72373015	HCPEpiC	choroid plexus:	n/a
4	chr2:72372965-72373015	MCF10A-Er-Src	breast:	n/a
5	chr2:72372965-72373015	H1-hESC	embryonic stem cell:	embryo
6	chr2:72372965-72373015	ovcar-3	ovarian:	n/a
7	chr2:72372965-72373015	HRPEpiC	eye:	n/a
8	chr2:72372965-72373015	HPAEpiC	pulmonary alveolar:	n/a
9	chr2:72372965-72373015	SK-N-MC	brain:	n/a
10	chr2:72372965-72373015	BJ	skin:	n/a
11	chr2:72372965-72373015	HRE	kidney:	n/a
12	chr2:72372965-72373015	MCF-7	breast:	n/a
13	chr2:72372965-72373015	IMR90	lung:	fetal
14	chr2:72372965-72373015	PANC-1	pancreas:	n/a
15	chr2:72372965-72373015	BE2_C	brain:	n/a
16	chr2:72372965-72373015	AoSMC	blood vessel:	n/a
17	chr2:72372965-72373015	PrEC	prostate:	n/a
18	chr2:72372965-72373015	CMK	blood:	n/a
19	chr2:72372965-72373015	HNPCEpiC	eye:	n/a
20	chr2:72372965-72373015	Jurkat	blood:	n/a
21	chr2:72372965-72373015	AG09319	gingival:	n/a
22	chr2:72372965-72373015	T-47D	breast:	n/a
23	chr2:72372965-72373015	HEEpiC	esophagus:	n/a
24	chr2:72372965-72373015	ECC-1	luminal epithelium:	n/a
25	chr2:72372965-72373015	Hela-S3	cervix:	n/a
26	chr2:72372965-72373015	GM12878	blood:	n/a
27	chr2:72372965-72373015	HCF	heart:	n/a
28	chr2:72372965-72373015	GM12891	blood:	n/a
29	chr2:72372965-72373015	HRCEpiC	kidney:	n/a
30	chr2:72372965-72373015	SAEC	small airway:	n/a
31	chr2:72372965-72373015	PFSK-1	brain:	n/a
32	chr2:72372965-72373015	RPTEC	kidney:	n/a
33	chr2:72372965-72373015	Caco-2	colon:	n/a
34	chr2:72372965-72373015	U87	brain:	n/a
35	chr2:72372965-72373015	SKMC	muscle:	n/a
36	chr2:72372965-72373015	AG04449	skin:	fetal
37	chr2:72372965-72373015	GM12892	blood:	n/a
38	chr2:72372965-72373015	SK-N-SH	brain:	n/a
39	chr2:72372965-72373015	HL-60	blood:	n/a
40	chr2:72372965-72373015	HCT-116	colon:	n/a
41	chr2:72372965-72373015	LNCaP	prostate:	n/a
42	chr2:72372965-72373015	HCM	heart:	n/a
43	chr2:72372965-72373015	NHBE	bronchial:	n/a
44	chr2:72372965-72373015	AG09309	skin:	n/a
45	chr2:72372965-72373015	HEK293	kidney:	embryo
46	chr2:72372965-72373015	HMEC	breast:	n/a
47	chr2:72372965-72373015	NHDF-neo	bronchial:	n/a
48	chr2:72372965-72373015	A549	lung:	n/a
49	chr2:72372965-72373015	NT2-D1	testis:	n/a
50	chr2:72372965-72373015	HUVEC	blood vessel:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:72371800..72374684-chr2:72379552..72382497,3	MCF-7	breast:
2	chr2:72019367..72021904-chr2:72372231..72374911,2	MCF-7	breast:
3	chr2:72368510..72373839-chr2:72374615..72379122,7	MCF-7	breast:

Variant related genes	Relation type
CYP26B1	TF binding region
CYP26B1	CpG island
ENSG00000003137	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10166057	0.93[ASN][1000 genomes]
rs10202129	1.00[JPT][hapmap]
rs13407599	0.80[EUR][1000 genomes]
rs2901091	0.82[EUR][1000 genomes]
rs3768638	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3768639	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3768641	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs62150093	0.83[ASN][1000 genomes]
rs6546745	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6546746	1.00[JPT][hapmap]
rs6546747	0.88[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs6710195	0.82[EUR][1000 genomes]
rs6710373	0.82[EUR][1000 genomes]
rs6738598	0.82[EUR][1000 genomes]
rs6738942	0.80[EUR][1000 genomes]
rs7596302	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[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	nsv582207	chr2:72329603-72389334	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72369000-72377200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr2:72369800-72373400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
3	chr2:72369800-72375000	Bivalent Enhancer	Fetal Brain Male	brain
4	chr2:72369800-72375600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
5	chr2:72370000-72373600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr2:72370000-72375600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
7	chr2:72370000-72377400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr2:72370400-72376600	Active TSS	Aorta	Aorta
9	chr2:72370600-72373200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:72370600-72375600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
11	chr2:72370600-72376400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
12	chr2:72371000-72373000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:72371000-72373600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr2:72371000-72375600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:72371200-72373000	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:72371200-72373000	Active TSS	Brain Substantia Nigra	brain
17	chr2:72371200-72373200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:72371400-72373000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:72371400-72373000	Active TSS	Brain Anterior Caudate	brain
20	chr2:72371400-72373000	Enhancers	Small Intestine	intestine
21	chr2:72371400-72373400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
22	chr2:72371400-72373600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr2:72371600-72373000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
24	chr2:72371600-72373000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
25	chr2:72371600-72373000	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
26	chr2:72371600-72373000	Weak transcription	Fetal Heart	heart
27	chr2:72371600-72373000	Active TSS	A549	lung
28	chr2:72371600-72373000	Bivalent/Poised TSS	NHEK	skin
29	chr2:72371600-72373200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
30	chr2:72371600-72373200	Active TSS	Hela-S3	cervix
31	chr2:72371600-72373600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
32	chr2:72371600-72373600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:72371600-72373600	Bivalent/Poised TSS	Fetal Brain Female	brain
34	chr2:72371600-72376400	Active TSS	Ovary	ovary
35	chr2:72371800-72373000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:72371800-72373000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
37	chr2:72371800-72373000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:72371800-72373000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:72371800-72373000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:72371800-72373000	Flanking Bivalent TSS/Enh	HepG2	liver
41	chr2:72371800-72373200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:72371800-72373200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
43	chr2:72371800-72373200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
44	chr2:72371800-72373400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:72371800-72373400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:72371800-72373600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
47	chr2:72371800-72375400	Bivalent Enhancer	Spleen	Spleen
48	chr2:72371800-72375600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
49	chr2:72371800-72376600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr2:72372000-72373000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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