Variant report

Variant	rs9596078
Chromosome Location	chr13:49877403-49877404
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49870136..49872971-chr13:49876994..49878672,2	MCF-7	breast:
2	chr13:49874891..49877806-chr13:49883558..49885352,2	K562	blood:
3	chr13:49877297..49879495-chr13:49894000..49896980,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10459375	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10459376	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11838927	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11843587	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12385878	0.81[EUR][1000 genomes]
rs12585196	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1555672	0.81[EUR][1000 genomes]
rs1924659	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1924660	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1924661	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2038759	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2147398	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2181905	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2274149	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274150	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407521	0.88[EUR][1000 genomes]
rs2407607	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2407608	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407609	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087770	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3764131	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4245351	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4941637	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4942809	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4942811	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4942812	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4942815	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6561511	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs719614	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7320595	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7320745	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7326181	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7326191	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7328063	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330892	0.88[EUR][1000 genomes]
rs7334929	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7984689	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7988621	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7991918	0.81[ASN][1000 genomes]
rs7997545	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7999710	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9316434	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9316437	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9316439	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526533	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526534	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526535	0.88[ASN][1000 genomes]
rs9526537	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526538	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9526539	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535173	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535174	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535177	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535180	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535181	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535182	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535184	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535185	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535190	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535192	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535193	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535194	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535197	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535198	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9535199	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9535200	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9535201	0.85[AFR][1000 genomes]
rs9562873	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568174	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9568176	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568177	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568179	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568181	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568182	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9591249	0.89[EUR][1000 genomes]
rs9596077	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9596079	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9596080	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv832607	chr13:49756458-49920894	Flanking Bivalent TSS/Enh Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900069	chr13:49815405-49976393	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49826600-49877800	Weak transcription	Psoas Muscle	Psoas
2	chr13:49854000-49877600	Weak transcription	Left Ventricle	heart
3	chr13:49854000-49883000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr13:49867200-49884200	Weak transcription	Fetal Brain Female	brain
5	chr13:49869200-49879200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr13:49869600-49882200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr13:49871600-49880400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr13:49872200-49878600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr13:49873400-49877800	Weak transcription	NH-A	brain
10	chr13:49873600-49877600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr13:49873800-49877800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr13:49873800-49878000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr13:49874800-49878000	Enhancers	Fetal Thymus	thymus
14	chr13:49875000-49877800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr13:49875000-49878200	Enhancers	Brain Cingulate Gyrus	brain
16	chr13:49875200-49878200	Enhancers	Gastric	stomach
17	chr13:49875200-49880400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr13:49875400-49877800	Weak transcription	NHLF	lung
19	chr13:49875400-49878600	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr13:49875600-49878200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr13:49875600-49878200	Enhancers	Right Ventricle	heart
22	chr13:49875800-49877600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr13:49875800-49877600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr13:49875800-49877600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr13:49875800-49877600	Weak transcription	HUVEC	blood vessel
26	chr13:49875800-49877800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr13:49875800-49877800	Weak transcription	Esophagus	oesophagus
28	chr13:49875800-49877800	Weak transcription	Ovary	ovary
29	chr13:49875800-49877800	Weak transcription	HSMM	muscle
30	chr13:49875800-49878400	Enhancers	Brain Hippocampus Middle	brain
31	chr13:49875800-49878400	Enhancers	Brain Substantia Nigra	brain
32	chr13:49875800-49878400	Enhancers	Fetal Muscle Trunk	muscle
33	chr13:49875800-49879000	Weak transcription	Fetal Kidney	kidney
34	chr13:49875800-49879400	Enhancers	Brain Angular Gyrus	brain
35	chr13:49875800-49881400	Weak transcription	Fetal Lung	lung
36	chr13:49875800-49883800	Weak transcription	Fetal Intestine Small	intestine
37	chr13:49875800-49884000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr13:49875800-49884200	Weak transcription	Primary T cells from cord blood	blood
39	chr13:49875800-49887800	Weak transcription	Fetal Intestine Large	intestine
40	chr13:49875800-49887800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr13:49875800-49891000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr13:49876000-49877600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr13:49876000-49879800	Weak transcription	Primary B cells from cord blood	blood
44	chr13:49876000-49880000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr13:49876000-49881400	Weak transcription	Stomach Mucosa	stomach
46	chr13:49876000-49881600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr13:49876000-49882200	Weak transcription	Placenta	Placenta
48	chr13:49876000-49884000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr13:49876200-49877600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr13:49876200-49877600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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