Variant report

Variant	rs12519611
Chromosome Location	chr5:58594684-58594685
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1031197	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10491352	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10940644	0.81[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11744761	0.87[ASN][1000 genomes]
rs11954668	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11959132	0.80[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11959567	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12189022	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12518773	0.83[ASN][1000 genomes]
rs12521263	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522944	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1445948	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1445952	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1445953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1445954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1579848	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1579849	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16889479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16889499	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16889518	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17444185	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17528522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17528578	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17628114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17780175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1823070	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1838733	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1840846	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1867711	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1867712	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1947090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1947095	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2021775	1.00[JPT][hapmap]
rs2028836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081106	1.00[JPT][hapmap]
rs2409631	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4700325	1.00[JPT][hapmap]
rs4700328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6858946	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6877508	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6891161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7703022	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs7719441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1030117	chr5:58587672-58637179	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58583600-58596400	Weak transcription	Esophagus	oesophagus
2	chr5:58584000-58596400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58590200-58594800	Weak transcription	Gastric	stomach
4	chr5:58591200-58595600	Enhancers	Fetal Heart	heart
5	chr5:58591600-58596400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:58591600-58597600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:58592800-58597800	Weak transcription	Left Ventricle	heart
8	chr5:58593000-58594800	Weak transcription	Colonic Mucosa	Colon
9	chr5:58593000-58611200	Weak transcription	Right Ventricle	heart
10	chr5:58593200-58594800	Weak transcription	Fetal Kidney	kidney
11	chr5:58593200-58594800	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:58593200-58595200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr5:58593200-58595400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:58593200-58595400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr5:58593200-58595600	Enhancers	Colon Smooth Muscle	Colon
16	chr5:58593200-58596600	Weak transcription	HSMMtube	muscle
17	chr5:58593200-58598200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:58593200-58612600	Weak transcription	Fetal Lung	lung
19	chr5:58593200-58613400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr5:58593400-58594800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr5:58593400-58595200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:58593400-58595400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:58593400-58595600	Enhancers	HMEC	breast
24	chr5:58593400-58595800	Enhancers	HUVEC	blood vessel
25	chr5:58593400-58596600	Weak transcription	HSMM	muscle
26	chr5:58593400-58597000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:58593600-58595000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:58593600-58595600	Enhancers	Rectal Smooth Muscle	rectum
29	chr5:58593800-58594800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr5:58593800-58594800	Enhancers	A549	lung
31	chr5:58593800-58595000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:58593800-58595200	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr5:58593800-58595600	Enhancers	NHEK	skin
34	chr5:58593800-58596400	Weak transcription	Fetal Intestine Large	intestine
35	chr5:58593800-58604800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr5:58594000-58594800	Weak transcription	Small Intestine	intestine
37	chr5:58594000-58595200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr5:58594000-58595200	Enhancers	Psoas Muscle	Psoas
39	chr5:58594000-58596400	Weak transcription	Fetal Intestine Small	intestine
40	chr5:58594000-58612800	Weak transcription	Stomach Mucosa	stomach
41	chr5:58594200-58596400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr5:58594400-58594800	Flanking Active TSS	Hela-S3	cervix
43	chr5:58594400-58595000	Weak transcription	Right Atrium	heart
44	chr5:58594400-58606000	Weak transcription	Rectal Mucosa Donor 29	rectum

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