Variant report

Variant	rs173965
Chromosome Location	chr5:114908109-114908110
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	chr5:114645138..114646056-chr5:114908059..114908645,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10055677	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs12187973	0.85[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs13164545	0.84[CEU][hapmap]
rs171774	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap]
rs173966	0.94[ASN][1000 genomes]
rs187682	0.86[ASN][1000 genomes]
rs2169771	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2303747	0.81[CEU][hapmap]
rs2546486	0.96[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2546487	0.81[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap]
rs2559990	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs256942	0.89[GIH][hapmap]
rs256943	0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs256944	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs256945	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs256951	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs256954	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs256956	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs256959	0.83[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs256964	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap]
rs256968	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs256969	0.91[ASN][1000 genomes]
rs256970	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs256971	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256972	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256976	0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.82[ASN][1000 genomes]
rs256978	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256980	0.87[ASN][1000 genomes]
rs256984	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs256986	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs256987	0.95[ASN][1000 genomes]
rs256988	0.96[ASN][1000 genomes]
rs256991	0.96[ASN][1000 genomes]
rs256993	0.96[ASN][1000 genomes]
rs256994	0.83[ASN][1000 genomes]
rs256996	0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs256997	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs256998	0.94[ASN][1000 genomes]
rs387718	0.82[ASN][1000 genomes]
rs400570	0.91[GIH][hapmap]
rs415577	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs698365	0.91[GIH][hapmap]
rs698366	0.91[GIH][hapmap]
rs698367	0.81[CEU][hapmap]
rs813761	0.81[CHB][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv830455	chr5:114761542-114938284	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1032234	chr5:114785557-114911527	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1796164	chr5:114854685-114936768	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114894600-114908800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr5:114896200-114908400	Weak transcription	NH-A	brain
3	chr5:114901400-114922400	Weak transcription	Fetal Muscle Leg	muscle
4	chr5:114902400-114911200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:114904800-114911200	Weak transcription	HSMMtube	muscle
6	chr5:114906200-114909000	Enhancers	Brain Anterior Caudate	brain
7	chr5:114906200-114909000	Enhancers	Brain Hippocampus Middle	brain
8	chr5:114906200-114910600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr5:114906400-114908800	Enhancers	Brain Angular Gyrus	brain
10	chr5:114906400-114909000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:114906400-114909000	Enhancers	Brain Substantia Nigra	brain
12	chr5:114906400-114910400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:114906600-114908800	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr5:114906800-114908200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr5:114906800-114910200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:114907000-114908400	Enhancers	Brain Germinal Matrix	brain
17	chr5:114907000-114909000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:114907000-114909000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:114907400-114909000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:114907600-114908200	Weak transcription	HSMM	muscle
21	chr5:114907600-114908200	Weak transcription	HUVEC	blood vessel
22	chr5:114907600-114908800	Weak transcription	Pancreas	Pancrea
23	chr5:114907600-114911000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:114907800-114908400	Weak transcription	Psoas Muscle	Psoas
25	chr5:114907800-114908800	Enhancers	Brain Cingulate Gyrus	brain
26	chr5:114907800-114918200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr5:114908000-114908600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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