Variant report

Variant	rs9825103
Chromosome Location	chr3:196314211-196314212
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196312510..196315466-chr3:196332119..196334631,2	K562	blood:
2	chr3:196312738..196315414-chr3:196359776..196362202,2	K562	blood:
3	chr3:196310084..196313670-chr3:196313950..196316230,5	K562	blood:
4	chr3:196295473..196297972-chr3:196309898..196314847,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185798	Chromatin interaction
ENSG00000174013	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11185546	0.93[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs12634928	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12636646	0.86[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.80[TSI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12636666	0.86[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.80[TSI][hapmap]
rs1872353	0.93[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs2341337	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34676641	0.82[EUR][1000 genomes]
rs35827219	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6764637	0.82[EUR][1000 genomes]
rs6791472	0.82[EUR][1000 genomes]
rs6808029	0.82[EUR][1000 genomes]
rs7648453	0.82[EUR][1000 genomes]
rs9870529	0.86[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9825103	FBXO45	cis	Lymphoblastoid	GTEx
rs9825103	RNF168	cis	cerebellum	SCAN
rs9825103	ENSG00000174013	cis	multi-tissue	Pritchard
rs9825103	FBXO45	Cis_1M	lymphoblastoid	RTeQTL
rs9825103	MGC33212	cis	multi-tissue	Pritchard

Chromatin state (count:108 , 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	chr3:196297200-196315600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:196297200-196316800	Weak transcription	Brain Angular Gyrus	brain
12	chr3:196297200-196323000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:196297400-196318800	Weak transcription	Pancreas	Pancrea
14	chr3:196298000-196319400	Weak transcription	Fetal Brain Male	brain
15	chr3:196303400-196316400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:196304400-196314600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr3:196304400-196314800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:196305600-196320000	Weak transcription	NHDF-Ad	bronchial
19	chr3:196306400-196317800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:196306600-196325000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:196308000-196316000	Weak transcription	Spleen	Spleen
22	chr3:196308000-196316800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:196308000-196317400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:196308000-196320000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:196309200-196319600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:196309200-196322200	Weak transcription	Fetal Intestine Small	intestine
27	chr3:196309200-196323000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:196311000-196314600	Strong transcription	Primary B cells from cord blood	blood
29	chr3:196311000-196315600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:196311400-196319200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:196311400-196320400	Weak transcription	Gastric	stomach
32	chr3:196311600-196314800	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:196311600-196315000	Weak transcription	HMEC	breast
34	chr3:196311600-196315200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:196311600-196315200	Weak transcription	HSMM	muscle
36	chr3:196311600-196315400	Weak transcription	HUVEC	blood vessel
37	chr3:196311600-196315800	Weak transcription	Stomach Mucosa	stomach
38	chr3:196311600-196316000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:196311600-196316200	Weak transcription	Fetal Heart	heart
40	chr3:196311600-196316400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:196311600-196316800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:196311600-196316800	Weak transcription	GM12878-XiMat	blood
43	chr3:196311600-196317200	Weak transcription	Psoas Muscle	Psoas
44	chr3:196311600-196317200	Weak transcription	NHEK	skin
45	chr3:196311600-196317400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:196311600-196317600	Weak transcription	Placenta	Placenta
47	chr3:196311600-196318000	Weak transcription	Ovary	ovary
48	chr3:196311600-196323000	Weak transcription	Esophagus	oesophagus
49	chr3:196311600-196324800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:196312000-196317600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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