Variant report

Variant	rs13072038
Chromosome Location	chr3:135978797-135978798
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135914058..135916023-chr3:135977800..135980119,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12695645	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316214	1.00[ASN][1000 genomes]
rs13321721	1.00[ASN][1000 genomes]
rs1604793	1.00[ASN][1000 genomes]
rs17200216	0.88[EUR][1000 genomes]
rs17298525	1.00[ASN][1000 genomes]
rs17364492	1.00[ASN][1000 genomes]
rs28634226	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718456	1.00[ASN][1000 genomes]
rs34031772	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34168675	1.00[ASN][1000 genomes]
rs34282798	1.00[ASN][1000 genomes]
rs34324561	0.84[EUR][1000 genomes]
rs34428695	1.00[ASN][1000 genomes]
rs34757183	1.00[ASN][1000 genomes]
rs34913797	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35326900	1.00[ASN][1000 genomes]
rs35522825	1.00[ASN][1000 genomes]
rs66890203	1.00[ASN][1000 genomes]
rs6768743	1.00[ASN][1000 genomes]
rs67949818	1.00[ASN][1000 genomes]
rs6796523	0.96[EUR][1000 genomes]
rs9810051	0.86[EUR][1000 genomes]
rs9810789	1.00[ASN][1000 genomes]
rs9812579	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813115	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818056	1.00[ASN][1000 genomes]
rs9818536	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820621	0.86[EUR][1000 genomes]
rs9823373	1.00[ASN][1000 genomes]
rs9826454	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837158	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841529	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844666	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866840	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870825	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872178	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880211	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv933522	chr3:135968919-135981180	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
4	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 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	chr3:135970000-135980000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:135970200-135979000	Weak transcription	Esophagus	oesophagus
3	chr3:135970200-135980400	Weak transcription	Gastric	stomach
4	chr3:135970200-135984000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:135970200-135996000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:135970400-135979000	Weak transcription	HUVEC	blood vessel
7	chr3:135970400-135981600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:135970400-135995400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:135970600-135979200	Weak transcription	A549	lung
10	chr3:135970600-135979400	Weak transcription	HSMM	muscle
11	chr3:135970600-135979400	Weak transcription	NHDF-Ad	bronchial
12	chr3:135970600-135985200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:135970600-135985200	Weak transcription	HMEC	breast
14	chr3:135970600-135987600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:135970600-135998800	Weak transcription	Fetal Brain Male	brain
16	chr3:135970600-135999200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:135970600-135999200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:135970600-136039400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:135970800-135979200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:135970800-135981200	Weak transcription	Fetal Heart	heart
21	chr3:135970800-135986000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:135970800-135995400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:135970800-135998000	Weak transcription	Hela-S3	cervix
24	chr3:135973400-135984200	Strong transcription	Fetal Stomach	stomach
25	chr3:135974000-135983400	Strong transcription	Fetal Thymus	thymus
26	chr3:135974000-135986800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:135974000-135986800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:135974000-135989400	Strong transcription	Dnd41	blood
29	chr3:135974200-135982400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:135974200-135982800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:135974200-135983200	Strong transcription	Stomach Smooth Muscle	stomach
32	chr3:135974200-135983400	Strong transcription	Fetal Muscle Leg	muscle
33	chr3:135974200-135989600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:135974200-135989600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:135974400-135982600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:135974400-135983000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:135974400-135983000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:135974400-135983200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:135974400-135983600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr3:135974400-135984600	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:135974400-135984600	Strong transcription	Liver	Liver
42	chr3:135974400-135986400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:135974400-135989600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:135974600-135981600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:135974600-135981800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:135974600-135982400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:135974600-135982800	Strong transcription	Left Ventricle	heart
48	chr3:135974600-135983000	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:135974600-135983400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:135974600-135985200	Strong transcription	Primary monocytes fromperipheralblood	blood

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