Variant report

Variant	rs1486916
Chromosome Location	chr3:47822415-47822416
allele	G/T
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:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47809506..47818715-chr3:47820075..47824996,15	MCF-7	breast:
2	chr3:47017679..47019433-chr3:47821354..47822860,2	K562	blood:
3	chr3:47781011..47782804-chr3:47820824..47822711,2	K562	blood:
4	chr3:47820857..47823354-chr3:47836932..47839468,2	K562	blood:
5	chr3:47803866..47805515-chr3:47821094..47823324,2	K562	blood:
6	chr3:47555041..47556961-chr3:47821638..47825112,3	MCF-7	breast:
7	chr3:47807226..47809643-chr3:47821048..47823302,2	MCF-7	breast:
8	chr3:47821014..47824119-chr3:47842599..47847365,10	K562	blood:
9	chr3:47821496..47825290-chr3:47843622..47845759,4	MCF-7	breast:
10	chr3:47819738..47825460-chr3:47843094..47847845,6	K562	blood:
11	chr3:47787622..47789169-chr3:47820606..47823344,2	MCF-7	breast:
12	chr3:47821651..47823502-chr3:172427414..172429681,2	MCF-7	breast:
13	chr3:47820608..47822821-chr3:47870608..47873437,2	K562	blood:
14	chr3:47553771..47557534-chr3:47822005..47824702,4	K562	blood:
15	chr3:47617723..47621182-chr3:47821900..47825077,3	MCF-7	breast:
16	chr3:47821442..47824826-chr3:47842672..47846080,5	MCF-7	breast:
17	chr3:47821721..47824833-chr3:47865723..47867890,4	K562	blood:
18	chr3:47555068..47558623-chr3:47821026..47823771,5	K562	blood:
19	chr3:47822067..47822622-chr5:131825519..131826350,2	Hela-S3	cervix:
20	chr3:47579787..47581854-chr3:47822138..47824570,2	K562	blood:
21	chr3:47783474..47786163-chr3:47820894..47822857,2	MCF-7	breast:
22	chr3:47819996..47824833-chr3:47866390..47869916,6	K562	blood:
23	chr3:47750990..47753722-chr3:47821277..47822829,2	K562	blood:
24	chr3:47555986..47558236-chr3:47820565..47823335,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163832	Chromatin interaction
ENSG00000132153	Chromatin interaction
ENSG00000125347	Chromatin interaction
ENSG00000160799	Chromatin interaction
ENSG00000173473	Chromatin interaction
ENSG00000144959	Chromatin interaction
ENSG00000266443	Chromatin interaction
ENSG00000266457	Chromatin interaction
ENSG00000114646	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1038391	1.00[EUR][1000 genomes]
rs1060407	1.00[YRI][hapmap]
rs11130134	1.00[EUR][1000 genomes]
rs11707679	1.00[YRI][hapmap]
rs11711725	1.00[YRI][hapmap]
rs11712464	1.00[YRI][hapmap]
rs11714816	1.00[EUR][1000 genomes]
rs12635438	1.00[YRI][hapmap]
rs2170814	1.00[EUR][1000 genomes]
rs2351249	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2593817	1.00[AMR][1000 genomes]
rs319683	0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs319693	1.00[YRI][hapmap]
rs34675858	0.82[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4383546	1.00[EUR][1000 genomes]
rs4476528	1.00[AMR][1000 genomes]
rs4858833	1.00[EUR][1000 genomes]
rs4858834	1.00[EUR][1000 genomes]
rs4858855	1.00[EUR][1000 genomes]
rs4858863	1.00[YRI][hapmap]
rs55736379	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55808934	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442092	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6776963	1.00[YRI][hapmap]
rs73831515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831540	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831544	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629850	1.00[YRI][hapmap]
rs883662	1.00[YRI][hapmap]
rs9863220	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003072	chr3:47673628-47869154	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv876758	chr3:47681881-47842234	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
3	nsv876759	chr3:47725315-47830741	Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
4	nsv834679	chr3:47749475-47924006	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
5	nsv590233	chr3:47798700-47829277	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
6	nsv965333	chr3:47815622-47845296	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	esv3402580	chr3:47822248-47824246	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47820000-47825200	Active TSS	GM12878-XiMat	blood
2	chr3:47820200-47822600	Active TSS	Brain Germinal Matrix	brain
3	chr3:47820600-47823200	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr3:47820600-47823800	Active TSS	Fetal Brain Male	brain
5	chr3:47820800-47823000	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr3:47820800-47823800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:47820800-47824000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr3:47820800-47824200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:47821000-47822800	Active TSS	Right Atrium	heart
10	chr3:47821000-47824200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:47821000-47824200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:47821000-47824600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:47821200-47822600	Weak transcription	Small Intestine	intestine
14	chr3:47821200-47822600	Weak transcription	Spleen	Spleen
15	chr3:47821200-47822800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:47821200-47822800	Flanking Active TSS	Liver	Liver
17	chr3:47821200-47823400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:47821200-47823600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:47821200-47823800	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr3:47821200-47823800	Active TSS	Fetal Intestine Large	intestine
21	chr3:47821200-47823800	Active TSS	HMEC	breast
22	chr3:47821200-47823800	Active TSS	HSMMtube	muscle
23	chr3:47821200-47824000	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr3:47821200-47824000	Active TSS	Fetal Brain Female	brain
25	chr3:47821200-47824000	Active TSS	Thymus	Thymus
26	chr3:47821200-47824000	Active TSS	NHDF-Ad	bronchial
27	chr3:47821200-47824200	Active TSS	H1 Cell Line	embryonic stem cell
28	chr3:47821200-47824200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:47821200-47824200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:47821200-47824400	Active TSS	H9 Cell Line	embryonic stem cell
31	chr3:47821200-47824400	Active TSS	NHLF	lung
32	chr3:47821400-47822800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr3:47821400-47823400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:47821400-47823800	Active TSS	Muscle Satellite Cultured Cells	--
35	chr3:47821400-47823800	Active TSS	Fetal Intestine Small	intestine
36	chr3:47821400-47823800	Active TSS	Fetal Lung	lung
37	chr3:47821400-47823800	Active TSS	NH-A	brain
38	chr3:47821400-47824000	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr3:47821400-47824000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:47821400-47824200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:47821400-47824200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:47821400-47824200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:47821400-47824200	Active TSS	Fetal Stomach	stomach
44	chr3:47821400-47824400	Active TSS	A549	lung
45	chr3:47821400-47824600	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr3:47821400-47824600	Active TSS	Colonic Mucosa	Colon
47	chr3:47821400-47824600	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr3:47821600-47822800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr3:47821600-47823600	Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr3:47821600-47823600	Active TSS	Stomach Smooth Muscle	stomach

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