Variant report

Variant	rs12439825
Chromosome Location	chr15:35278475-35278476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:35277451..35279992-chr15:35357452..35360430,2	MCF-7	breast:
2	chr15:35276711..35279528-chr15:35281828..35283922,2	MCF-7	breast:
3	chr15:35272114..35275594-chr15:35276542..35279290,3	MCF-7	breast:
4	chr15:35260477..35263827-chr15:35276648..35278665,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000021776	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10152246	0.95[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10438394	0.96[ASN][1000 genomes]
rs10444812	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10519967	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap]
rs11073076	0.91[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs11629721	0.84[ASN][1000 genomes]
rs11635485	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11636350	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11855784	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs11857217	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs12441204	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs12442905	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs12591197	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12593603	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12593818	0.91[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap]
rs12708534	0.83[ASN][1000 genomes]
rs12899377	0.83[CHB][hapmap]
rs12901394	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12901466	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12901794	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12901991	0.86[CHB][hapmap]
rs12915053	0.80[ASN][1000 genomes]
rs12915493	0.95[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs12917386	0.86[CHB][hapmap]
rs1376784	0.91[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap]
rs16959966	0.86[CHB][hapmap]
rs2060809	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.85[ASN][1000 genomes]
rs2060810	0.95[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2060811	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2060812	0.94[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2290320	0.87[CHD][hapmap]
rs2305411	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28498500	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36067547	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3743121	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs3816447	0.91[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs3848167	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs4513050	0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4569214	0.85[CHB][hapmap]
rs4923817	0.91[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap]
rs4923845	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4923849	1.00[CHD][hapmap];0.94[MKK][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4924325	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs4924339	0.83[JPT][hapmap];0.88[MEX][hapmap]
rs4924344	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs4924357	0.91[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap]
rs4924369	0.91[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap]
rs6495724	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs6495728	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495729	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495730	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7164151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7164169	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7164266	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7164977	0.86[CHB][hapmap]
rs7167892	0.90[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap]
rs7170280	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7172507	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7177337	0.85[ASN][1000 genomes]
rs7177962	0.86[CHB][hapmap]
rs7179205	0.85[ASN][1000 genomes]
rs7179833	0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7181836	0.87[ASN][1000 genomes]
rs7182356	0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs8025770	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs8031861	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8033077	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8037610	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8040551	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs959478	0.86[CHB][hapmap]
rs963425	0.91[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap]
rs9806487	0.95[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs9920529	0.85[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	esv3350109	chr15:34668106-35534229	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv522411	chr15:34953986-35462981	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:35262000-35278600	Weak transcription	Gastric	stomach
2	chr15:35262400-35278600	Weak transcription	HSMMtube	muscle
3	chr15:35262400-35279000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:35262400-35279000	Weak transcription	Aorta	Aorta
5	chr15:35262600-35278600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr15:35262600-35278600	Weak transcription	Right Ventricle	heart
7	chr15:35262600-35278600	Weak transcription	Thymus	Thymus
8	chr15:35262600-35278800	Weak transcription	Esophagus	oesophagus
9	chr15:35262600-35278800	Weak transcription	Ovary	ovary
10	chr15:35267600-35278600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:35269600-35278600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:35271800-35278600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:35275000-35278600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:35275000-35278600	Weak transcription	Psoas Muscle	Psoas
15	chr15:35275200-35278800	Weak transcription	Colonic Mucosa	Colon
16	chr15:35275400-35278600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:35275400-35278600	Weak transcription	Fetal Thymus	thymus
18	chr15:35275400-35278600	Weak transcription	NHLF	lung
19	chr15:35276200-35278600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:35276200-35278800	Strong transcription	Fetal Muscle Leg	muscle
21	chr15:35276400-35278800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:35276600-35278600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr15:35276600-35278600	Weak transcription	NHDF-Ad	bronchial
24	chr15:35276600-35278600	Weak transcription	Osteobl	bone
25	chr15:35276600-35278800	Genic enhancers	Primary T cells fromperipheralblood	blood
26	chr15:35276600-35278800	Enhancers	Adipose Nuclei	Adipose
27	chr15:35276800-35278600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:35277000-35278600	Enhancers	Brain Anterior Caudate	brain
29	chr15:35277000-35278600	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr15:35277000-35278600	Enhancers	Duodenum Mucosa	Duodenum
31	chr15:35277000-35278600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr15:35277000-35278800	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr15:35277000-35278800	Genic enhancers	Primary T cells from cord blood	blood
34	chr15:35277000-35278800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr15:35277200-35278600	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr15:35277200-35278800	Enhancers	Brain Angular Gyrus	brain
37	chr15:35277200-35278800	Weak transcription	Placenta	Placenta
38	chr15:35277200-35279000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
39	chr15:35277200-35279000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr15:35277200-35279000	Weak transcription	Lung	lung
41	chr15:35277200-35279000	Enhancers	Pancreas	Pancrea
42	chr15:35277200-35279600	Flanking Active TSS	Liver	Liver
43	chr15:35277400-35278600	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr15:35277400-35278600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr15:35277400-35278600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:35277400-35278600	Enhancers	Fetal Brain Female	brain
47	chr15:35277400-35278600	Weak transcription	Fetal Stomach	stomach
48	chr15:35277400-35278600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr15:35277400-35278600	Weak transcription	Small Intestine	intestine
50	chr15:35277400-35278800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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