Variant report

Variant	rs13073885
Chromosome Location	chr3:119865160-119865161
allele	C/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119811328..119819569-chr3:119859303..119870611,43	MCF-7	breast:
2	chr3:119865007..119867802-chr3:119897494..119899931,3	MCF-7	breast:
3	chr3:119865137..119868181-chr3:119877404..119880372,3	MCF-7	breast:
4	chr3:119862753..119866394-chr3:119887362..119889316,3	MCF-7	breast:
5	chr3:119829682..119832031-chr3:119864501..119867434,2	MCF-7	breast:
6	chr3:119809272..119819238-chr3:119861129..119869186,35	MCF-7	breast:
7	chr3:119864581..119866968-chr3:119914610..119916835,2	MCF-7	breast:
8	chr3:119864838..119867291-chr3:119874320..119877276,3	MCF-7	breast:
9	chr3:119864495..119866427-chr3:119878369..119880021,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1079784	0.87[EUR][1000 genomes]
rs10934510	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10934520	0.85[EUR][1000 genomes]
rs13061630	1.00[JPT][hapmap]
rs13079094	0.88[EUR][1000 genomes]
rs13095684	0.83[AMR][1000 genomes]
rs1492272	1.00[JPT][hapmap]
rs2029607	1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs34032950	0.86[EUR][1000 genomes]
rs34537735	0.81[EUR][1000 genomes]
rs34720062	0.86[EUR][1000 genomes]
rs35280462	0.86[EUR][1000 genomes]
rs35791817	0.85[EUR][1000 genomes]
rs35902169	0.85[EUR][1000 genomes]
rs35977875	0.86[EUR][1000 genomes]
rs4146299	1.00[JPT][hapmap]
rs4146300	1.00[JPT][hapmap]
rs4563433	0.95[CEU][hapmap]
rs4676703	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438575	1.00[JPT][hapmap]
rs6776878	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6781123	0.82[AMR][1000 genomes]
rs6792814	0.88[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7630226	0.86[EUR][1000 genomes]
rs7633395	0.88[EUR][1000 genomes]
rs7634938	0.84[EUR][1000 genomes]
rs7641727	0.96[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer 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	29 gene(s)	inside rSNPs	diseases
6	nsv3967	chr3:119857708-119903115	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13073885	KPNA1	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119861200-119866000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:119862000-119867800	Enhancers	Placenta	Placenta
3	chr3:119862200-119866400	Enhancers	HepG2	liver
4	chr3:119862400-119865200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:119862600-119868000	Enhancers	HMEC	breast
6	chr3:119863000-119865200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:119863000-119865200	Enhancers	NHDF-Ad	bronchial
8	chr3:119863000-119867200	Enhancers	Placenta Amnion	Placenta Amnion
9	chr3:119863000-119867800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:119863400-119867600	Enhancers	Fetal Intestine Small	intestine
11	chr3:119863600-119865400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:119863600-119865800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:119863600-119866000	Weak transcription	Adipose Nuclei	Adipose
14	chr3:119863600-119866000	Weak transcription	Fetal Lung	lung
15	chr3:119863600-119866000	Weak transcription	Left Ventricle	heart
16	chr3:119863600-119866000	Weak transcription	Lung	lung
17	chr3:119863600-119866200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:119863800-119866200	Weak transcription	Fetal Heart	heart
19	chr3:119864200-119865200	Flanking Active TSS	NHEK	skin
20	chr3:119864200-119868000	Enhancers	Fetal Intestine Large	intestine
21	chr3:119864400-119866200	Enhancers	Esophagus	oesophagus
22	chr3:119864600-119865200	Flanking Active TSS	Hela-S3	cervix
23	chr3:119864600-119866200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:119864600-119866400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr3:119864600-119871800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:119864800-119865200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:119864800-119865200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:119864800-119866000	Weak transcription	HUVEC	blood vessel
29	chr3:119864800-119866400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:119864800-119866400	Weak transcription	Stomach Mucosa	stomach
31	chr3:119864800-119866800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:119864800-119871600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:119865000-119866000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr3:119865000-119866000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:119865000-119866000	Weak transcription	Right Atrium	heart
36	chr3:119865000-119866000	Weak transcription	A549	lung
37	chr3:119865000-119866200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:119865000-119866200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:119865000-119866200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:119865000-119866400	Weak transcription	HSMMtube	muscle
41	chr3:119865000-119870800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:119865000-119870800	Weak transcription	Osteobl	bone

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