Variant report

Variant	rs1396497
Chromosome Location	chr5:115427416-115427417
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	chr5:115418542..115422487-chr5:115423504..115427625,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271918	Chromatin interaction
ENSG00000145781	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10040031	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10045890	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10051539	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10054121	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs10055039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10057577	0.82[ASN][1000 genomes]
rs10060732	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10072350	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10072373	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10072417	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10072430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10075082	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10478275	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10478283	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10900713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11241361	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11241362	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11241363	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1133186	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs11738779	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11742121	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12055304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13190092	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1588268	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2063252	0.80[ASN][1000 genomes]
rs2136211	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2202816	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2416425	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2416431	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs34471954	0.84[ASN][1000 genomes]
rs3933997	0.80[ASN][1000 genomes]
rs4920903	0.84[ASN][1000 genomes]
rs4920904	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs4920905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4920906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4921056	0.85[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs4921057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4921061	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4921064	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4921066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6594942	0.89[ASN][1000 genomes]
rs6594943	0.83[ASN][1000 genomes]
rs6594946	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6594947	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6594950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6594953	0.81[ASN][1000 genomes]
rs6594954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6594955	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6863734	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6872757	0.88[ASN][1000 genomes]
rs6877029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6878279	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6881750	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6896119	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6896147	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6896571	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7704903	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7734133	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9326993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1027418	chr5:115206256-115446861	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv515611	chr5:115208843-115428381	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1024008	chr5:115222974-115431050	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1027117	chr5:115222974-115442883	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	esv2763487	chr5:115222986-115442895	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv462400	chr5:115223504-115428381	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv599478	chr5:115223504-115428381	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1030480	chr5:115228889-115446861	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv599479	chr5:115233116-115450969	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv1015976	chr5:115236239-115434163	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv537868	chr5:115236239-115434163	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv882736	chr5:115254723-115552945	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
14	nsv882737	chr5:115263853-115552945	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
15	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
16	nsv527320	chr5:115382097-115573543	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv1027266	chr5:115382704-115501792	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
19	nsv1032199	chr5:115384131-115525738	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
20	esv2830404	chr5:115386661-115490546	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	nsv1019972	chr5:115386860-115563533	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
22	nsv537869	chr5:115386860-115563533	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
23	nsv1018861	chr5:115397834-115563533	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
24	nsv537870	chr5:115397834-115563533	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115421200-115428600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:115421400-115428200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:115421400-115428400	Weak transcription	Lung	lung
4	chr5:115421400-115428600	Weak transcription	Gastric	stomach
5	chr5:115421400-115428800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:115421400-115433400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:115421400-115444200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:115421400-115446400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:115421400-115446400	Weak transcription	Esophagus	oesophagus
10	chr5:115421600-115428200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:115421600-115428200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:115421600-115428200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr5:115421600-115428200	Weak transcription	Ovary	ovary
14	chr5:115421600-115428400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:115421600-115428600	Weak transcription	Psoas Muscle	Psoas
16	chr5:115421600-115436600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:115421800-115428200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:115421800-115428200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:115421800-115428200	Weak transcription	HSMMtube	muscle
20	chr5:115421800-115428600	Weak transcription	Thymus	Thymus
21	chr5:115421800-115428800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr5:115421800-115428800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:115421800-115448000	Weak transcription	Aorta	Aorta
24	chr5:115422000-115428000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:115422000-115428000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:115422000-115428000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr5:115422000-115428000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr5:115422000-115428000	Weak transcription	Brain Anterior Caudate	brain
29	chr5:115422000-115428000	Weak transcription	Brain Substantia Nigra	brain
30	chr5:115422000-115428000	Weak transcription	A549	lung
31	chr5:115422000-115428000	Weak transcription	NH-A	brain
32	chr5:115422000-115428200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr5:115422000-115428200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr5:115422000-115428200	Weak transcription	Brain Hippocampus Middle	brain
35	chr5:115422000-115428200	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:115422000-115428200	Weak transcription	NHDF-Ad	bronchial
37	chr5:115422000-115428400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr5:115422000-115428400	Weak transcription	Brain Angular Gyrus	brain
39	chr5:115422000-115428400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr5:115422000-115428400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:115422000-115428400	Weak transcription	Fetal Kidney	kidney
42	chr5:115422000-115428400	Weak transcription	Fetal Stomach	stomach
43	chr5:115422000-115428400	Weak transcription	Osteobl	bone
44	chr5:115422000-115428600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr5:115422000-115428600	Weak transcription	Colonic Mucosa	Colon
46	chr5:115422000-115428600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr5:115422000-115428800	Weak transcription	Fetal Brain Male	brain
48	chr5:115422000-115428800	Weak transcription	Fetal Brain Female	brain
49	chr5:115422000-115428800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr5:115422000-115433600	Weak transcription	Stomach Mucosa	stomach

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