Variant report

Variant	rs17008864
Chromosome Location	chr2:73442516-73442517
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	SREBP1	chr2:73440797-73442976	GM12878	blood:	n/a	n/a
2	MXI1	chr2:73440958-73442626	IMR90	lung:	n/a	n/a
3	STAT3	chr2:73442180-73442574	MCF10A-Er-Src	breast:	n/a	n/a
4	MXI1	chr2:73440860-73443005	SK-N-SH	brain:	n/a	n/a
5	MYC	chr2:73440953-73442828	A549	lung:	n/a	chr2:73441535-73441544 chr2:73441404-73441414 chr2:73441994-73442002
6	MAZ	chr2:73442340-73442548	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:73439579..73446812-chr2:73458193..73462998,13	MCF-7	breast:
2	chr2:73440196..73443079-chr2:73443307..73449769,10	MCF-7	breast:
3	chr2:73427265..73431524-chr2:73439833..73442659,3	K562	blood:
4	chr2:73440673..73443060-chr2:73492840..73495806,2	MCF-7	breast:
5	chr2:73113964..73115739-chr2:73439855..73442724,2	MCF-7	breast:

Variant related genes	Relation type
SMYD5	TF binding region
ENSG00000135632	Chromatin interaction
ENSG00000116096	Chromatin interaction
ENSG00000163013	Chromatin interaction
ENSG00000214513	Chromatin interaction
ENSG00000135624	Chromatin interaction
ENSG00000135617	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10048666	0.89[ASN][1000 genomes]
rs10048720	0.89[ASN][1000 genomes]
rs10048837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10048838	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10175626	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs10185970	0.89[ASN][1000 genomes]
rs10189022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs10193579	0.89[ASN][1000 genomes]
rs10195007	1.00[ASN][1000 genomes]
rs10195282	1.00[ASN][1000 genomes]
rs10198711	1.00[ASN][1000 genomes]
rs11884073	0.89[ASN][1000 genomes]
rs11888772	1.00[ASN][1000 genomes]
rs11893547	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11894877	0.81[AFR][1000 genomes]
rs11902788	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs13009208	1.00[ASN][1000 genomes]
rs13385938	1.00[ASN][1000 genomes]
rs13386236	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13404992	1.00[ASN][1000 genomes]
rs13409784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13415504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs13423796	0.89[ASN][1000 genomes]
rs13424035	1.00[ASN][1000 genomes]
rs17008829	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17008862	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2043092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288632	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28464603	1.00[ASN][1000 genomes]
rs28494567	1.00[ASN][1000 genomes]
rs3768636	1.00[ASN][1000 genomes]
rs3820701	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs546576	1.00[JPT][hapmap]
rs56276021	0.88[AFR][1000 genomes]
rs57321619	0.89[ASN][1000 genomes]
rs60913601	1.00[ASN][1000 genomes]
rs61534579	1.00[ASN][1000 genomes]
rs6757079	1.00[ASN][1000 genomes]
rs72809926	0.84[AFR][1000 genomes]
rs72903461	0.89[ASN][1000 genomes]
rs7580825	1.00[CHB][hapmap]
rs7594590	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv2776	chr2:73431854-73482304	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	26 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	chr2:73440800-73442600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:73441000-73442600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr2:73441000-73442600	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr2:73441000-73442800	Active TSS	Fetal Brain Female	brain
5	chr2:73441000-73442800	Active TSS	HSMM	muscle
6	chr2:73441000-73443000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:73441400-73442600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:73441400-73442800	Active TSS	NH-A	brain
9	chr2:73441600-73443000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr2:73441800-73442600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:73441800-73442600	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr2:73441800-73442600	Flanking Active TSS	HUVEC	blood vessel
13	chr2:73441800-73442800	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr2:73441800-73443000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:73441800-73443000	Flanking Active TSS	Dnd41	blood
16	chr2:73442000-73442600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr2:73442000-73442600	Enhancers	Primary B cells from cord blood	blood
18	chr2:73442000-73442600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:73442000-73442600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr2:73442000-73442600	Weak transcription	Lung	lung
21	chr2:73442000-73442600	Flanking Active TSS	NHEK	skin
22	chr2:73442000-73442800	Enhancers	Primary B cells from peripheral blood	blood
23	chr2:73442000-73442800	Enhancers	Gastric	stomach
24	chr2:73442000-73442800	Enhancers	Stomach Mucosa	stomach
25	chr2:73442000-73442800	Flanking Active TSS	Osteobl	bone
26	chr2:73442000-73443000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:73442000-73443000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:73442000-73443000	Flanking Active TSS	Hela-S3	cervix
29	chr2:73442000-73444600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:73442000-73445400	Weak transcription	Aorta	Aorta
31	chr2:73442000-73445600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:73442000-73446000	Weak transcription	Esophagus	oesophagus
33	chr2:73442000-73446000	Weak transcription	Spleen	Spleen
34	chr2:73442000-73446200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:73442000-73447000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:73442000-73447200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:73442000-73447600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:73442000-73447800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr2:73442000-73453800	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr2:73442200-73442600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:73442200-73442600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:73442200-73442600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr2:73442200-73442600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr2:73442200-73442600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr2:73442200-73442600	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr2:73442200-73442600	Enhancers	Fetal Stomach	stomach
47	chr2:73442200-73442800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr2:73442200-73442800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:73442200-73442800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr2:73442200-73442800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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