Variant report

Variant	rs10513495
Chromosome Location	chr3:156468970-156468971
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:2)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156392442..156394339-chr3:156468772..156471259,2	MCF-7	breast:
2	chr3:156467361..156469859-chr3:156528012..156530054,3	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSR3-3	chr3:156468884-156468972	ENSG00000240875
2	lnc-SSR3-3	chr3:156468884-156468972	ENSG00000240875
3	lnc-SSR3-3	chr3:156468884-156468972	NONHSAT092863
4	lnc-SSR3-3	chr3:156468884-156468972	NR_038387

No data

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction
ENSG00000230457	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12636629	0.89[EUR][1000 genomes]
rs1367312	0.90[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1529581	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16826869	0.93[TSI][hapmap]
rs16826877	0.93[TSI][hapmap]
rs17373227	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41366145	0.89[EUR][1000 genomes]
rs4364127	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55686038	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56128116	0.87[EUR][1000 genomes]
rs56152727	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56245561	0.90[EUR][1000 genomes]
rs56354026	0.92[EUR][1000 genomes]
rs56357051	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56836190	0.84[EUR][1000 genomes]
rs56960846	0.84[EUR][1000 genomes]
rs57483705	0.89[EUR][1000 genomes]
rs58263861	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58822703	0.97[EUR][1000 genomes]
rs59689193	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73012038	0.81[EUR][1000 genomes]
rs73012046	0.81[EUR][1000 genomes]
rs73013957	0.87[EUR][1000 genomes]
rs73019737	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73019748	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73019749	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs891463	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs919520	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][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	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10513495	LINC00886	cis	Thyroid	GTEx
rs10513495	SMC4	cis	parietal	SCAN
rs10513495	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156466200-156470200	Enhancers	Fetal Muscle Leg	muscle
2	chr3:156466600-156469600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:156466800-156469000	Enhancers	H1 Cell Line	embryonic stem cell
4	chr3:156466800-156469000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:156466800-156469000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr3:156466800-156469000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:156466800-156469400	Enhancers	Brain Cingulate Gyrus	brain
8	chr3:156466800-156469600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr3:156466800-156469600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:156466800-156469600	Enhancers	Fetal Heart	heart
11	chr3:156466800-156469800	Enhancers	Fetal Kidney	kidney
12	chr3:156466800-156469800	Enhancers	Fetal Lung	lung
13	chr3:156466800-156471200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:156467000-156469000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:156467000-156469200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:156467000-156469400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:156467000-156469400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:156467000-156469600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:156467000-156469600	Enhancers	Fetal Muscle Trunk	muscle
20	chr3:156467000-156469800	Enhancers	Brain Substantia Nigra	brain
21	chr3:156467000-156470200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:156467000-156470200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:156467000-156470200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:156467200-156469400	Enhancers	H9 Cell Line	embryonic stem cell
25	chr3:156467400-156469200	Enhancers	Brain Hippocampus Middle	brain
26	chr3:156467600-156470200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:156467800-156469000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:156467800-156469400	Flanking Active TSS	HSMMtube	muscle
29	chr3:156467800-156469600	Enhancers	Brain Germinal Matrix	brain
30	chr3:156467800-156470000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr3:156467800-156470200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:156467800-156470200	Enhancers	Fetal Stomach	stomach
33	chr3:156468000-156469200	Enhancers	Right Atrium	heart
34	chr3:156468000-156471000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr3:156468200-156469200	Weak transcription	Fetal Intestine Large	intestine
36	chr3:156468200-156469400	Enhancers	Brain Angular Gyrus	brain
37	chr3:156468200-156469400	Flanking Active TSS	HMEC	breast
38	chr3:156468200-156469400	Flanking Active TSS	HSMM	muscle
39	chr3:156468200-156469600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr3:156468200-156469600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:156468200-156469600	Enhancers	Lung	lung
42	chr3:156468200-156469600	Flanking Active TSS	NHEK	skin
43	chr3:156468200-156469800	Flanking Active TSS	NH-A	brain
44	chr3:156468400-156469000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:156468400-156469200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr3:156468400-156469200	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr3:156468400-156469400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr3:156468400-156469600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr3:156468400-156469600	Enhancers	Fetal Intestine Small	intestine
50	chr3:156468400-156470000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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