Variant report

Variant	rs12656253
Chromosome Location	chr5:96337154-96337155
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	chr5:96336570..96338080-chr5:96338829..96341118,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12657704	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2194245	0.82[ASN][1000 genomes]
rs2287902	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303210	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3797795	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797797	0.93[ASN][1000 genomes]
rs3797798	0.86[CHB][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797850	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3806940	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55767008	0.93[ASN][1000 genomes]
rs55870170	0.93[ASN][1000 genomes]
rs58477147	1.00[AMR][1000 genomes]
rs58748938	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60280354	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6862188	0.87[EUR][1000 genomes]
rs73141135	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73141187	1.00[AMR][1000 genomes]
rs769336	1.00[AMR][1000 genomes]
rs769338	1.00[AMR][1000 genomes]
rs7723473	1.00[AMR][1000 genomes]
rs7728347	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv948703	chr5:96078309-96368839	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1027472	chr5:96081592-96337550	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1028741	chr5:96082401-96372165	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv949058	chr5:96082433-96390619	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv598963	chr5:96084776-96363407	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96304800-96346600	Weak transcription	Lung	lung
2	chr5:96304800-96359600	Weak transcription	Hela-S3	cervix
3	chr5:96313400-96342600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:96313400-96342600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr5:96314000-96360200	Weak transcription	Fetal Brain Male	brain
6	chr5:96314200-96343600	Strong transcription	Primary B cells from peripheral blood	blood
7	chr5:96314200-96344000	Strong transcription	Primary B cells from cord blood	blood
8	chr5:96314200-96347600	Strong transcription	Fetal Thymus	thymus
9	chr5:96314400-96343800	Strong transcription	Dnd41	blood
10	chr5:96314800-96343200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr5:96314800-96343800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr5:96315400-96374800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:96315600-96353400	Weak transcription	Pancreas	Pancrea
14	chr5:96315600-96358600	Weak transcription	Brain Substantia Nigra	brain
15	chr5:96316000-96338400	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:96316000-96360000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr5:96316400-96346600	Weak transcription	NH-A	brain
18	chr5:96320000-96357600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:96321200-96344600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr5:96321600-96344800	Weak transcription	Small Intestine	intestine
21	chr5:96322200-96348600	Weak transcription	Fetal Kidney	kidney
22	chr5:96322200-96349800	Weak transcription	Psoas Muscle	Psoas
23	chr5:96322400-96353600	Weak transcription	Right Ventricle	heart
24	chr5:96322400-96358600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:96322400-96359600	Weak transcription	Gastric	stomach
26	chr5:96323800-96342200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:96325800-96338200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr5:96326400-96346600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr5:96326800-96340200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:96327000-96339600	Weak transcription	Ovary	ovary
31	chr5:96327400-96339600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:96329800-96358800	Weak transcription	Brain Germinal Matrix	brain
33	chr5:96330000-96359800	Weak transcription	Aorta	Aorta
34	chr5:96330200-96340400	Weak transcription	Osteobl	bone
35	chr5:96330400-96359400	Weak transcription	Fetal Brain Female	brain
36	chr5:96330600-96339000	Weak transcription	Fetal Lung	lung
37	chr5:96330600-96339800	Weak transcription	Brain Angular Gyrus	brain
38	chr5:96330600-96353600	Weak transcription	Esophagus	oesophagus
39	chr5:96330800-96339400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:96331600-96339400	Weak transcription	Brain Anterior Caudate	brain
41	chr5:96331600-96340000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:96331600-96344600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:96331600-96356200	Weak transcription	Fetal Stomach	stomach
44	chr5:96331600-96357800	Weak transcription	Spleen	Spleen
45	chr5:96331800-96338400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr5:96331800-96349800	Weak transcription	HSMM	muscle
47	chr5:96333400-96344600	Strong transcription	GM12878-XiMat	blood
48	chr5:96333600-96343000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:96333600-96374000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:96333800-96339600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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