Variant report

Variant	rs1058600
Chromosome Location	chr5:115166713-115166714
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:114970097..114971014-chr5:115166622..115167477,4	MCF-7	breast:
2	chr5:115166705..115169190-chr5:115172735..115175090,2	MCF-7	breast:
3	chr5:114970792..114971474-chr5:115166118..115167014,2	MCF-7	breast:
4	chr5:114969735..114972107-chr5:115165947..115167928,2	MCF-7	breast:
5	chr5:114970131..114970716-chr5:115166661..115167300,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP3S1-1	chr5:115166259-115167054	NONHSAT103329

No data

Variant related genes	Relation type
ENSG00000145782	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10434761	0.97[ASN][1000 genomes]
rs10751460	0.81[ASN][1000 genomes]
rs11241336	0.82[ASN][1000 genomes]
rs11241337	0.81[ASN][1000 genomes]
rs12189155	0.85[ASN][1000 genomes]
rs12332653	0.80[ASN][1000 genomes]
rs12513891	0.81[ASN][1000 genomes]
rs12514553	0.81[ASN][1000 genomes]
rs12517882	0.82[ASN][1000 genomes]
rs12520248	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12521324	0.88[ASN][1000 genomes]
rs13157716	0.82[ASN][1000 genomes]
rs13174348	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs152368	0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs152369	0.81[ASN][1000 genomes]
rs152397	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs152398	0.83[ASN][1000 genomes]
rs154757	0.92[ASN][1000 genomes]
rs154759	0.85[ASN][1000 genomes]
rs171809	0.84[CHD][hapmap]
rs2080902	0.82[ASN][1000 genomes]
rs26529	0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs26531	0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs26533	0.96[ASN][1000 genomes]
rs26534	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.96[ASN][1000 genomes]
rs26535	0.96[ASN][1000 genomes]
rs26536	0.90[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs26537	0.86[CHB][hapmap];0.89[CHD][hapmap];0.88[ASN][1000 genomes]
rs26538	0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs34850	0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs34851	0.97[ASN][1000 genomes]
rs34852	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs34869	0.95[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs35053218	0.91[ASN][1000 genomes]
rs35179959	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35501287	0.83[ASN][1000 genomes]
rs35903246	0.98[ASN][1000 genomes]
rs3797568	0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs3797569	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs3797570	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40095	0.96[ASN][1000 genomes]
rs4920892	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57633641	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59750231	0.82[ASN][1000 genomes]
rs61381571	0.83[ASN][1000 genomes]
rs6594906	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6872406	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6879485	0.80[ASN][1000 genomes]
rs6880889	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71581214	0.81[ASN][1000 genomes]
rs7707539	0.81[ASN][1000 genomes]
rs7713314	0.83[ASN][1000 genomes]
rs7726368	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1058600	ATG12	cis	cerebellum	SCAN
rs1058600	EPB41L4A	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115152800-115171200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:115153200-115169600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:115153600-115172400	Weak transcription	Fetal Brain Male	brain
4	chr5:115154400-115169600	Weak transcription	Brain Angular Gyrus	brain
5	chr5:115154600-115173000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:115154800-115169200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr5:115155000-115169200	Weak transcription	Brain Anterior Caudate	brain
8	chr5:115155000-115169800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr5:115155000-115174400	Weak transcription	Fetal Heart	heart
10	chr5:115155200-115167200	Weak transcription	Brain Substantia Nigra	brain
11	chr5:115155200-115169400	Weak transcription	Brain Germinal Matrix	brain
12	chr5:115157600-115171000	Weak transcription	Thymus	Thymus
13	chr5:115159000-115169000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr5:115160000-115169600	Weak transcription	Psoas Muscle	Psoas
15	chr5:115160600-115169800	Weak transcription	Left Ventricle	heart
16	chr5:115161400-115169600	Weak transcription	Ovary	ovary
17	chr5:115161800-115176200	Weak transcription	Gastric	stomach
18	chr5:115162000-115174400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:115162000-115176200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:115162000-115176600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr5:115162200-115167200	Weak transcription	K562	blood
22	chr5:115162400-115171800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:115162600-115175600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:115162800-115168200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:115162800-115170400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr5:115163000-115168000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr5:115163000-115169600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:115163000-115171000	Weak transcription	Hela-S3	cervix
29	chr5:115163000-115173400	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr5:115163000-115176400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr5:115163200-115168200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr5:115163200-115171000	Weak transcription	HSMMtube	muscle
33	chr5:115163200-115174000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:115163400-115167200	Strong transcription	Fetal Muscle Leg	muscle
35	chr5:115163400-115167600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr5:115163400-115168200	Strong transcription	NH-A	brain
37	chr5:115163400-115173800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr5:115163400-115173800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr5:115163400-115173800	Strong transcription	NHDF-Ad	bronchial
40	chr5:115163400-115174200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:115163600-115168200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:115163600-115171200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr5:115163600-115173200	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr5:115163800-115167400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr5:115163800-115167400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:115163800-115167600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr5:115163800-115167800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:115163800-115168200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:115163800-115168200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:115163800-115169600	Weak transcription	Right Ventricle	heart

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