Variant report

Variant	rs17400736
Chromosome Location	chr2:153572943-153572944
allele	A/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	chr2:153572495-153576612	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr2:153572377-153574144	MCF10A-Er-Src	breast:	n/a	chr2:153573447-153573457
3	CHD1	chr2:153572366-153573129	H1-hESC	embryonic stem cell:	n/a	n/a
4	MYC	chr2:153572355-153572958	K562	blood:	n/a	n/a
5	POLR2A	chr2:153572295-153576273	H1-hESC	embryonic stem cell:	n/a	n/a
6	SREBP1	chr2:153570771-153575432	GM12878	blood:	n/a	n/a
7	MXI1	chr2:153572226-153576757	SK-N-SH	brain:	n/a	chr2:153575089-153575098
8	CTCF	chr2:153572331-153572964	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr2:153572488-153577031	K562	blood:	n/a	n/a
10	POLR2A	chr2:153572534-153576259	PBDE	blood:	n/a	n/a
11	MXI1	chr2:153572315-153576784	K562	blood:	n/a	chr2:153575089-153575098
12	MAZ	chr2:153572924-153575976	IMR90	lung:	n/a	chr2:153573447-153573457
13	POLR2A	chr2:153572690-153577175	GM12891	blood:	n/a	n/a
14	CTCF	chr2:153571731-153576009	A549	lung:	n/a	chr2:153573370-153573388
15	TBL1XR1	chr2:153572395-153573299	K562	blood:	n/a	n/a
16	CTCF	chr2:153572840-153572990	BE2_C	brain:	n/a	n/a
17	HCFC1	chr2:153572226-153575918	Hela-S3	cervix:	n/a	n/a
18	MAFF	chr2:153572510-153573865	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:153572649..153576015-chr2:157196773..157199686,4	K562	blood:
2	chr2:153031056..153034207-chr2:153571978..153575897,4	K562	blood:
3	chr2:153030783..153033861-chr2:153572629..153575835,5	MCF-7	breast:

Variant related genes	Relation type
ARL6IP6	TF binding region
PRPF40A	TF binding region
ENSG00000115145	Chromatin interaction
ENSG00000153234	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10208744	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1036525	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10497116	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13010731	1.00[YRI][hapmap]
rs13012521	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs13021349	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs16831548	1.00[YRI][hapmap]
rs17328643	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17400610	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1986744	1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2304558	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs34043301	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs34121167	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs34419942	0.92[ASN][1000 genomes]
rs6738344	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[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	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153558200-153573000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:153558800-153573000	Weak transcription	Aorta	Aorta
3	chr2:153558800-153573200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:153558800-153573400	Weak transcription	Spleen	Spleen
5	chr2:153566800-153573400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:153568800-153573200	Weak transcription	Lung	lung
7	chr2:153571800-153573000	Enhancers	Small Intestine	intestine
8	chr2:153571800-153573400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:153572000-153573000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:153572000-153573200	Enhancers	Stomach Mucosa	stomach
11	chr2:153572000-153573800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:153572000-153576400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:153572000-153576400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:153572000-153576400	Active TSS	K562	blood
15	chr2:153572200-153576400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:153572200-153576400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:153572200-153576400	Active TSS	HMEC	breast
18	chr2:153572200-153576800	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr2:153572200-153577000	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr2:153572400-153573000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr2:153572400-153573000	Enhancers	Primary B cells from peripheral blood	blood
22	chr2:153572400-153573000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr2:153572400-153573000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr2:153572400-153573000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:153572400-153573000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr2:153572400-153573000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr2:153572400-153573000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:153572400-153573000	Flanking Active TSS	Brain Angular Gyrus	brain
29	chr2:153572400-153573000	Enhancers	Esophagus	oesophagus
30	chr2:153572400-153573000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr2:153572400-153573000	Enhancers	Placenta	Placenta
32	chr2:153572400-153573000	Enhancers	Gastric	stomach
33	chr2:153572400-153573000	Enhancers	Pancreas	Pancrea
34	chr2:153572400-153573000	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr2:153572400-153573000	Flanking Active TSS	HUVEC	blood vessel
36	chr2:153572400-153573000	Flanking Active TSS	NH-A	brain
37	chr2:153572400-153573000	Flanking Active TSS	NHEK	skin
38	chr2:153572400-153573200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:153572400-153573200	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr2:153572400-153573200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr2:153572400-153573200	Flanking Active TSS	Osteobl	bone
42	chr2:153572400-153573400	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr2:153572400-153573400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr2:153572400-153573400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr2:153572400-153573400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:153572400-153573400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:153572400-153573400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:153572400-153573400	Flanking Active TSS	Liver	Liver
49	chr2:153572400-153573400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr2:153572400-153573400	Flanking Active TSS	Rectal Smooth Muscle	rectum

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