Variant report

Variant	rs1872353
Chromosome Location	chr3:196312951-196312952
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	chr3:196312510..196315466-chr3:196332119..196334631,2	K562	blood:
2	chr3:196307955..196310042-chr3:196312339..196313885,2	K562	blood:
3	chr3:196310084..196313670-chr3:196313950..196316230,5	K562	blood:
4	chr3:196295521..196297345-chr3:196311801..196313995,2	K562	blood:
5	chr3:196312738..196315414-chr3:196359776..196362202,2	K562	blood:
6	chr3:196294648..196297345-chr3:196309580..196313995,4	K562	blood:
7	chr3:196311659..196313218-chr3:196314271..196315787,2	MCF-7	breast:
8	chr3:196295473..196297972-chr3:196309898..196314847,6	MCF-7	breast:
9	chr3:196310004..196313820-chr3:196314591..196318789,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000185798	Chromatin interaction
ENSG00000174013	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11185546	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12485589	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12634928	0.94[EUR][1000 genomes]
rs12636646	0.93[CEU][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs12636666	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2341337	0.93[CEU][hapmap];0.83[CHB][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34676641	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35827219	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66570007	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6764637	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791472	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808029	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430950	0.82[MEX][hapmap];0.82[MKK][hapmap]
rs7648453	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648887	1.00[ASW][hapmap]
rs970414	0.86[AMR][1000 genomes]
rs9825103	0.93[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs9870529	0.93[CEU][hapmap];0.82[CHB][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS 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	84 gene(s)	inside rSNPs	diseases
5	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	nsv1010643	chr3:196288064-196788645	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
12	nsv965250	chr3:196311218-196313117	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv878188	chr3:196312124-196553867	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1872353	FBXO45	Cis_1M	lymphoblastoid	RTeQTL
rs1872353	RNF168	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196296600-196320200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:196296800-196316800	Weak transcription	Right Ventricle	heart
3	chr3:196297000-196314400	Weak transcription	Brain Anterior Caudate	brain
4	chr3:196297000-196316000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:196297000-196316200	Weak transcription	Right Atrium	heart
6	chr3:196297000-196317000	Weak transcription	NHLF	lung
7	chr3:196297000-196317800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:196297000-196318000	Weak transcription	Colonic Mucosa	Colon
9	chr3:196297000-196320400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:196297200-196313200	Weak transcription	Fetal Kidney	kidney
11	chr3:196297200-196315600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:196297200-196316800	Weak transcription	Brain Angular Gyrus	brain
13	chr3:196297200-196323000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:196297400-196313800	Weak transcription	Small Intestine	intestine
15	chr3:196297400-196318800	Weak transcription	Pancreas	Pancrea
16	chr3:196298000-196319400	Weak transcription	Fetal Brain Male	brain
17	chr3:196298600-196313000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:196303400-196316400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:196304000-196314200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:196304200-196314000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr3:196304200-196314200	Strong transcription	Dnd41	blood
22	chr3:196304400-196313600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:196304400-196313600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:196304400-196313600	Strong transcription	Fetal Thymus	thymus
25	chr3:196304400-196313600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr3:196304400-196313800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:196304400-196314000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:196304400-196314000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:196304400-196314000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:196304400-196314000	Strong transcription	Duodenum Mucosa	Duodenum
31	chr3:196304400-196314600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr3:196304400-196314800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:196305600-196320000	Weak transcription	NHDF-Ad	bronchial
34	chr3:196306200-196314200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:196306400-196317800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:196306600-196325000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr3:196308000-196316000	Weak transcription	Spleen	Spleen
38	chr3:196308000-196316800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:196308000-196317400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:196308000-196320000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:196308200-196313600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:196308800-196314000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:196309000-196314200	Strong transcription	Hela-S3	cervix
44	chr3:196309200-196319600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:196309200-196322200	Weak transcription	Fetal Intestine Small	intestine
46	chr3:196309200-196323000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:196309400-196313000	Weak transcription	Brain Substantia Nigra	brain
48	chr3:196309600-196313200	Weak transcription	Brain Germinal Matrix	brain
49	chr3:196310600-196313000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:196310600-196313800	Strong transcription	Fetal Muscle Trunk	muscle

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