Variant report

Variant	rs2252651
Chromosome Location	chr10:28032136-28032137
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	TAF1	chr10:28031881-28032788	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr10:28031607-28032650	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr10:28031140-28033015	HCT-116	colon:	n/a	n/a
4	POLR2A	chr10:28032104-28032234	ProgFib	skin:	n/a	n/a
5	TEAD4	chr10:28031919-28032405	ECC-1	luminal epithelium:	n/a	n/a
6	SIN3A	chr10:28031928-28032705	H1-hESC	embryonic stem cell:	n/a	n/a
7	SUZ12	chr10:28031619-28036341	NT2-D1	testis:	n/a	n/a
8	ZBTB7A	chr10:28031255-28032788	ECC-1	luminal epithelium:	n/a	chr10:28032132-28032140
9	TAF1	chr10:28031016-28032615	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr10:28031032-28032833	HCT-116	colon:	n/a	n/a
11	POLR2A	chr10:28032002-28032355	MCF-7	breast:	n/a	n/a
12	MAX	chr10:28031912-28032919	ECC-1	luminal epithelium:	n/a	chr10:28032074-28032083
13	MAX	chr10:28030985-28032974	ECC-1	luminal epithelium:	n/a	chr10:28031404-28031413 chr10:28032074-28032083
14	CTBP2	chr10:28029973-28035811	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr10:28031863-28032789	Gliobla	brain:	n/a	n/a
16	TCF12	chr10:28031086-28032517	ECC-1	luminal epithelium:	n/a	chr10:28031522-28031529 chr10:28031518-28031528 chr10:28031521-28031531
17	ZBTB7A	chr10:28031277-28033843	ECC-1	luminal epithelium:	n/a	chr10:28032132-28032140 chr10:28033575-28033584
18	TBP	chr10:28031843-28032363	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr10:28031056-28032766	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:28030500..28032197-chr10:28034707..28036331,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230500	TF binding region
ENSG00000150051	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1907376	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1907386	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1907390	0.82[EUR][1000 genomes]
rs1907391	0.82[EUR][1000 genomes]
rs1907392	0.93[EUR][1000 genomes]
rs2246842	0.81[EUR][1000 genomes]
rs2246903	0.80[EUR][1000 genomes]
rs2451915	0.82[EUR][1000 genomes]
rs2451916	0.82[EUR][1000 genomes]
rs2451917	0.82[EUR][1000 genomes]
rs2451919	0.83[EUR][1000 genomes]
rs2451920	0.84[EUR][1000 genomes]
rs2451925	0.81[EUR][1000 genomes]
rs2451927	0.81[EUR][1000 genomes]
rs2492903	0.81[EUR][1000 genomes]
rs2492904	0.81[EUR][1000 genomes]
rs2492911	0.90[EUR][1000 genomes]
rs2492912	0.82[EUR][1000 genomes]
rs2492913	0.83[EUR][1000 genomes]
rs2492914	0.83[EUR][1000 genomes]
rs2492915	0.82[EUR][1000 genomes]
rs2492916	0.83[EUR][1000 genomes]
rs2492917	0.84[EUR][1000 genomes]
rs2637287	0.81[EUR][1000 genomes]
rs2637288	0.81[EUR][1000 genomes]
rs2637289	0.81[EUR][1000 genomes]
rs2637290	0.84[EUR][1000 genomes]
rs2637291	0.81[EUR][1000 genomes]
rs2637293	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2637297	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2637303	0.82[EUR][1000 genomes]
rs2637304	0.82[EUR][1000 genomes]
rs2637314	0.82[EUR][1000 genomes]
rs2637320	0.84[EUR][1000 genomes]
rs2637321	0.85[EUR][1000 genomes]
rs2637322	0.84[EUR][1000 genomes]
rs2637323	0.84[EUR][1000 genomes]
rs2637324	0.84[EUR][1000 genomes]
rs2637327	0.89[EUR][1000 genomes]
rs2637333	0.85[EUR][1000 genomes]
rs2782338	0.83[EUR][1000 genomes]
rs2782339	0.84[EUR][1000 genomes]
rs2782340	0.84[EUR][1000 genomes]
rs2782341	0.84[EUR][1000 genomes]
rs2782342	0.84[EUR][1000 genomes]
rs2815477	0.97[EUR][1000 genomes]
rs2815478	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2815479	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2815482	0.81[EUR][1000 genomes]
rs2815484	0.81[EUR][1000 genomes]
rs2815485	0.81[EUR][1000 genomes]
rs2815486	0.81[EUR][1000 genomes]
rs2815487	0.81[EUR][1000 genomes]
rs2815488	0.84[EUR][1000 genomes]
rs2815489	0.84[EUR][1000 genomes]
rs2815490	0.81[EUR][1000 genomes]
rs2815491	0.84[EUR][1000 genomes]
rs2815493	0.84[EUR][1000 genomes]
rs2815494	0.84[EUR][1000 genomes]
rs2815499	0.83[EUR][1000 genomes]
rs2815559	0.88[EUR][1000 genomes]
rs2815560	0.82[EUR][1000 genomes]
rs2815561	0.82[EUR][1000 genomes]
rs2815562	0.82[EUR][1000 genomes]
rs2815564	0.89[EUR][1000 genomes]
rs2815565	0.82[EUR][1000 genomes]
rs2815566	0.81[EUR][1000 genomes]
rs2815569	0.83[EUR][1000 genomes]
rs2815570	0.83[EUR][1000 genomes]
rs2815571	0.83[EUR][1000 genomes]
rs2815573	0.83[EUR][1000 genomes]
rs2815574	0.85[EUR][1000 genomes]
rs2815575	0.85[EUR][1000 genomes]
rs2815576	0.85[EUR][1000 genomes]
rs2815577	0.84[EUR][1000 genomes]
rs2999980	0.83[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	esv3368825	chr10:27864181-28043820	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv831813	chr10:28017606-28200651	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28029800-28032600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr10:28029800-28033200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr10:28029800-28035800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr10:28029800-28036000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr10:28030000-28032800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr10:28030000-28033400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr10:28030000-28033600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr10:28030000-28036600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr10:28030200-28032800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr10:28030200-28036200	Bivalent Enhancer	Fetal Brain Male	brain
11	chr10:28030200-28036400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr10:28030400-28032200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr10:28030400-28033200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
14	chr10:28030400-28033400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr10:28030600-28032200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
16	chr10:28030600-28032800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr10:28030600-28033200	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr10:28030600-28035400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr10:28030800-28032600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
20	chr10:28030800-28032800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr10:28030800-28032800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
22	chr10:28030800-28033000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
23	chr10:28030800-28033400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
24	chr10:28030800-28033800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr10:28030800-28035000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
26	chr10:28030800-28035600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
27	chr10:28030800-28035800	Active TSS	Aorta	Aorta
28	chr10:28031000-28032200	Active TSS	Rectal Smooth Muscle	rectum
29	chr10:28031000-28032200	Active TSS	Hela-S3	cervix
30	chr10:28031000-28032400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
31	chr10:28031000-28032600	Active TSS	Brain Substantia Nigra	brain
32	chr10:28031000-28032600	Bivalent/Poised TSS	Fetal Lung	lung
33	chr10:28031000-28032800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
34	chr10:28031000-28033000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr10:28031000-28033600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
36	chr10:28031000-28033600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr10:28031000-28033600	Active TSS	Right Atrium	heart
38	chr10:28031000-28035400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
39	chr10:28031000-28035400	Active TSS	Ovary	ovary
40	chr10:28031200-28032200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr10:28031200-28032200	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
42	chr10:28031200-28032200	Active TSS	Brain Anterior Caudate	brain
43	chr10:28031200-28032400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr10:28031200-28032400	Bivalent/Poised TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr10:28031200-28032600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr10:28031200-28032600	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr10:28031200-28032600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr10:28031200-28032800	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr10:28031200-28032800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
50	chr10:28031200-28032800	Active TSS	NHDF-Ad	bronchial

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