Variant report

Variant	rs13074515
Chromosome Location	chr3:28306022-28306023
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:28305069..28306910-chr3:28307661..28310186,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10510606	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10510610	0.86[CEU][hapmap];0.95[MEX][hapmap]
rs11129312	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11129313	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11129314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11129317	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11708368	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11708635	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11717202	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11921526	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12106746	0.86[CEU][hapmap]
rs12106806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs12107183	1.00[CHB][hapmap]
rs12107556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs12485652	0.86[CEU][hapmap];0.95[MEX][hapmap]
rs12485853	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12485858	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12488712	0.86[CEU][hapmap];0.95[MEX][hapmap]
rs12491905	0.86[CEU][hapmap]
rs12493720	0.86[CEU][hapmap]
rs12493797	0.86[CEU][hapmap];0.91[MEX][hapmap]
rs12495684	0.84[CEU][hapmap]
rs12497510	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13068978	0.86[CEU][hapmap]
rs13069450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs13069777	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13073936	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13085236	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13085477	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13092179	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13095609	0.86[CEU][hapmap];0.90[MEX][hapmap]
rs13099977	0.93[CEU][hapmap]
rs1599951	0.85[MEX][hapmap]
rs1606391	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17639954	0.86[CEU][hapmap]
rs1870258	0.86[CEU][hapmap];0.86[MEX][hapmap]
rs34109684	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34692982	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35504778	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35813951	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4393865	0.86[CEU][hapmap];0.85[MEX][hapmap]
rs4552313	0.93[CEU][hapmap];0.86[MEX][hapmap]
rs4680746	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4680912	0.91[CEU][hapmap]
rs6780084	1.00[CHB][hapmap]
rs6782956	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6785465	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6792110	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6792215	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6794980	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[LWK][hapmap]
rs6795634	1.00[CHB][hapmap]
rs6798266	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6805638	0.93[CEU][hapmap]
rs6809706	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MKK][hapmap]
rs6809917	1.00[CHB][hapmap]
rs7624015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs7624111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][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	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28283800-28311400	Weak transcription	Lung	lung
2	chr3:28284000-28309600	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:28284000-28313800	Weak transcription	Ovary	ovary
4	chr3:28284000-28317200	Weak transcription	Gastric	stomach
5	chr3:28284400-28311000	Weak transcription	Fetal Intestine Small	intestine
6	chr3:28284400-28312600	Weak transcription	Fetal Lung	lung
7	chr3:28284400-28321800	Weak transcription	NHLF	lung
8	chr3:28284600-28307200	Weak transcription	Fetal Intestine Large	intestine
9	chr3:28284600-28311200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:28285600-28315400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:28285800-28311000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:28286000-28307200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:28287600-28317000	Weak transcription	Pancreas	Pancrea
14	chr3:28288600-28311200	Weak transcription	Esophagus	oesophagus
15	chr3:28291400-28311200	Weak transcription	Aorta	Aorta
16	chr3:28292800-28311000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:28293600-28311200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:28293800-28309800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:28294000-28309200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:28294200-28314400	Weak transcription	HepG2	liver
21	chr3:28294400-28313800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:28294400-28314200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:28294600-28313800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:28294800-28313800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:28294800-28316400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:28295000-28312200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:28295600-28313800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:28295600-28318200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr3:28298200-28309000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:28300000-28313800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:28300600-28311400	Weak transcription	Brain Anterior Caudate	brain
32	chr3:28301000-28313800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:28301800-28314000	Weak transcription	Brain Angular Gyrus	brain
34	chr3:28302200-28313800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr3:28302600-28309400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:28302600-28313800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:28303000-28314600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr3:28303000-28316800	Weak transcription	Right Ventricle	heart
39	chr3:28303200-28310000	Weak transcription	Psoas Muscle	Psoas
40	chr3:28303400-28322200	Weak transcription	Small Intestine	intestine
41	chr3:28303600-28313800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:28303600-28340600	Weak transcription	NHEK	skin
43	chr3:28303800-28307000	Weak transcription	Brain Germinal Matrix	brain
44	chr3:28303800-28311200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:28303800-28311400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:28303800-28320800	Weak transcription	Placenta	Placenta
47	chr3:28304000-28313000	Weak transcription	Fetal Kidney	kidney
48	chr3:28304000-28314000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:28304200-28306400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:28304200-28313800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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