Variant report

Variant	rs10058407
Chromosome Location	chr5:112418385-112418386
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	chr5:112372883..112375761-chr5:112416823..112419304,2	K562	blood:
2	chr5:112417847..112420032-chr5:112422512..112424237,2	MCF-7	breast:

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10036854	0.81[ASN][1000 genomes]
rs10039618	0.86[CHB][hapmap]
rs10045658	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10053994	0.97[ASN][1000 genomes]
rs10063834	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10077067	0.87[CHB][hapmap]
rs10078431	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10223151	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10223152	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10477486	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10478102	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10478106	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11241190	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11744218	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744817	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs11744828	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11744956	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11746908	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs11750093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11960706	0.92[CHB][hapmap];0.97[ASN][1000 genomes]
rs12513669	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13173830	0.87[CEU][hapmap]
rs13174818	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227947	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2227950	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28535973	0.80[ASN][1000 genomes]
rs28620751	0.80[ASN][1000 genomes]
rs28645351	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28774401	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs33551	0.82[CHB][hapmap]
rs33556	0.81[CHB][hapmap]
rs36182962	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3890775	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3890776	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4235788	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4283779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4397121	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4463174	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4645326	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4705758	0.86[CHB][hapmap]
rs56054154	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6594672	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6594673	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6594675	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6594679	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6594680	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6859485	0.92[CHB][hapmap]
rs6859562	0.81[CHB][hapmap]
rs6859813	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861166	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6861336	0.81[CHB][hapmap]
rs6862481	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6863319	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6865444	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6865585	0.82[ASN][1000 genomes]
rs6866442	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6866566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6866706	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6866718	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6869383	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6869399	0.81[CEU][hapmap]
rs6873623	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6874220	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6874314	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6874595	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6874727	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6878846	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6879138	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6879589	0.87[CHB][hapmap]
rs6879633	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6879634	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6879942	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6882155	0.87[CHB][hapmap]
rs6882309	0.81[ASN][1000 genomes]
rs6882689	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6888031	0.81[ASN][1000 genomes]
rs6893389	0.81[CHB][hapmap]
rs6894700	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6898297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7708475	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7713290	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7713336	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7714010	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7714160	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7714275	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7714334	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7714349	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7714363	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7714492	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7714725	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7728858	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7728921	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7730767	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs7732048	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7732198	0.81[CHB][hapmap]
rs7734411	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7734511	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7736823	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737329	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9326874	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9326875	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[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	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv599395	chr5:112370311-112428869	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1018344	chr5:112390951-112458853	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112371400-112423800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:112379600-112424200	Weak transcription	Psoas Muscle	Psoas
3	chr5:112384000-112453000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:112391600-112439000	Weak transcription	Gastric	stomach
5	chr5:112395600-112420400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:112399000-112432800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:112399800-112441800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:112400800-112423800	Weak transcription	Aorta	Aorta
9	chr5:112402600-112425600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:112403800-112418400	Weak transcription	Brain Substantia Nigra	brain
11	chr5:112404000-112426000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr5:112404400-112428000	Weak transcription	Placenta	Placenta
13	chr5:112404400-112436800	Weak transcription	Fetal Brain Male	brain
14	chr5:112404800-112425400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr5:112409000-112419600	Weak transcription	Fetal Heart	heart
16	chr5:112411000-112431800	Weak transcription	Spleen	Spleen
17	chr5:112411200-112425800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr5:112411200-112443400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:112411600-112425800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr5:112411800-112420400	Weak transcription	Pancreas	Pancrea
21	chr5:112411800-112428000	Weak transcription	Fetal Intestine Large	intestine
22	chr5:112412000-112435200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr5:112412200-112432400	Weak transcription	Fetal Intestine Small	intestine
24	chr5:112414200-112425600	Weak transcription	Brain Hippocampus Middle	brain
25	chr5:112416200-112421000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr5:112416600-112418600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
27	chr5:112416600-112420800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:112416600-112421000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:112416600-112421000	Strong transcription	Ovary	ovary
30	chr5:112416600-112421000	Strong transcription	Stomach Smooth Muscle	stomach
31	chr5:112416600-112421200	Strong transcription	Fetal Muscle Leg	muscle
32	chr5:112416600-112422600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:112416600-112422800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:112416800-112418400	Enhancers	HSMM	muscle
35	chr5:112416800-112418800	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:112417000-112418400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:112417000-112418600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:112417000-112419400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:112417000-112420800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr5:112417200-112418400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:112417400-112418400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:112417400-112418600	Genic enhancers	NHEK	skin
43	chr5:112417400-112420400	Strong transcription	Fetal Lung	lung
44	chr5:112417400-112420600	Strong transcription	Fetal Stomach	stomach
45	chr5:112417400-112423400	Strong transcription	Esophagus	oesophagus
46	chr5:112417600-112418400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:112417600-112418400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr5:112417600-112418400	Enhancers	Brain Anterior Caudate	brain
49	chr5:112417600-112418600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr5:112417600-112418600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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