Variant report

Variant	rs9877670
Chromosome Location	chr3:142444514-142444515
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142312229..142317018-chr3:142442889..142445391,9	K562	blood:
2	chr3:142443679..142445893-chr3:142461230..142463554,2	K562	blood:
3	chr3:142443512..142446497-chr3:142575988..142578278,2	K562	blood:
4	chr3:142442417..142444804-chr3:142718685..142721847,4	K562	blood:
5	chr3:142313378..142316741-chr3:142442748..142446550,8	K562	blood:
6	chr3:142314524..142316871-chr3:142442608..142445149,2	MCF-7	breast:
7	chr3:142297625..142299268-chr3:142441632..142445353,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000120756	Chromatin interaction
ENSG00000163714	Chromatin interaction
ENSG00000268129	Chromatin interaction
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10049098	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10049364	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10935469	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12330897	0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs12330901	1.00[AMR][1000 genomes]
rs13320613	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13322816	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13325615	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13434361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16834067	1.00[AMR][1000 genomes]
rs16852648	1.00[AMR][1000 genomes]
rs16852649	1.00[AMR][1000 genomes]
rs16852658	1.00[AMR][1000 genomes]
rs1916641	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28373594	1.00[AMR][1000 genomes]
rs28460347	1.00[AMR][1000 genomes]
rs28505293	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28564963	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28572271	1.00[AMR][1000 genomes]
rs28678273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28728040	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58015805	1.00[AMR][1000 genomes]
rs6798447	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72988606	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72988611	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72988625	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72990716	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72992624	1.00[AMR][1000 genomes]
rs72992644	1.00[AMR][1000 genomes]
rs72992647	1.00[AMR][1000 genomes]
rs72992650	1.00[AMR][1000 genomes]
rs73002086	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73002087	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7622773	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7637053	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7638554	0.93[AFR][1000 genomes]
rs7641418	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9289650	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9809475	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9810360	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9810606	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9819681	1.00[AMR][1000 genomes]
rs9823492	0.93[YRI][hapmap]
rs9826191	1.00[AMR][1000 genomes]
rs9827373	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9836232	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9837730	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9839771	1.00[AMR][1000 genomes]
rs9846572	1.00[AMR][1000 genomes]
rs9847616	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9850432	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9863330	1.00[AMR][1000 genomes]
rs9867286	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9867886	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9875489	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9877174	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9879367	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882985	0.81[AFR][1000 genomes];1.00[AMR][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	nsv591920	chr3:142411200-142496951	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv521098	chr3:142411200-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv518623	chr3:142417070-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142442200-142444600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:142442200-142444600	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr3:142442200-142444600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:142442200-142444800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:142442200-142444800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:142442200-142444800	Active TSS	K562	blood
7	chr3:142442200-142445000	Active TSS	A549	lung
8	chr3:142442400-142444600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:142442400-142444600	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:142442400-142444600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:142442400-142444600	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr3:142442400-142444600	Active TSS	Fetal Brain Male	brain
13	chr3:142442400-142444600	Active TSS	Fetal Kidney	kidney
14	chr3:142442400-142444800	Active TSS	H1 Cell Line	embryonic stem cell
15	chr3:142442400-142444800	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr3:142442400-142444800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:142442400-142444800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:142442400-142445000	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr3:142442600-142444600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr3:142442600-142444600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:142442600-142444600	Active TSS	NHLF	lung
22	chr3:142443800-142444600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:142443800-142444600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr3:142443800-142445200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:142444000-142444600	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr3:142444000-142444600	Enhancers	Dnd41	blood
27	chr3:142444000-142452600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:142444200-142444600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:142444200-142444600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr3:142444200-142444600	Enhancers	Adipose Nuclei	Adipose
31	chr3:142444200-142444600	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr3:142444200-142444600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr3:142444200-142444800	Active TSS	HepG2	liver
34	chr3:142444200-142445000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:142444200-142445000	Active TSS	Fetal Brain Female	brain
36	chr3:142444200-142445200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:142444200-142467400	Weak transcription	HSMM	muscle
38	chr3:142444400-142444600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:142444400-142444600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:142444400-142444600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr3:142444400-142444600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:142444400-142444600	Active TSS	Brain Anterior Caudate	brain
43	chr3:142444400-142444600	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr3:142444400-142444600	Enhancers	Colon Smooth Muscle	Colon
45	chr3:142444400-142444600	Flanking Active TSS	HMEC	breast
46	chr3:142444400-142444600	Enhancers	NH-A	brain
47	chr3:142444400-142444600	Flanking Active TSS	NHDF-Ad	bronchial
48	chr3:142444400-142444600	Enhancers	NHEK	skin
49	chr3:142444400-142444800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:142444400-142445000	Enhancers	Duodenum Smooth Muscle	Duodenum

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