Variant report

Variant	rs9846449
Chromosome Location	chr3:139074837-139074838
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:139073347..139076472-chr3:139106877..139110723,3	K562	blood:
2	chr3:139073016..139076494-chr3:139077200..139080091,3	MCF-7	breast:
3	chr3:139072091..139074896-chr3:139076494..139078712,3	K562	blood:
4	chr3:139061820..139064876-chr3:139073197..139076620,4	MCF-7	breast:
5	chr3:139072517..139075084-chr3:139096841..139099787,2	MCF-7	breast:
6	chr3:139074489..139078704-chr3:139090415..139094288,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248932	Chromatin interaction
ENSG00000252245	Chromatin interaction
ENSG00000184432	Chromatin interaction
ENSG00000175110	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12695695	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13325144	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs28545366	1.00[AFR][1000 genomes]
rs34654084	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35586329	1.00[AFR][1000 genomes]
rs71314515	0.83[AFR][1000 genomes]
rs9820144	1.00[AFR][1000 genomes]
rs9821204	1.00[ASW][hapmap]
rs9839834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9874641	1.00[GIH][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.83[AMR][1000 genomes]
rs9878661	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv4034	chr3:139034976-139080133	Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9846449	ATP1B3	cis	cerebellum	SCAN
rs9846449	PAQR9	cis	cerebellum	SCAN
rs9846449	BPESC1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139064200-139089200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:139064400-139097200	Strong transcription	Fetal Muscle Leg	muscle
3	chr3:139064800-139094600	Strong transcription	Primary B cells from cord blood	blood
4	chr3:139065000-139096200	Strong transcription	Fetal Intestine Large	intestine
5	chr3:139065000-139101200	Strong transcription	Primary T cells from cord blood	blood
6	chr3:139065000-139103800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:139065000-139103800	Strong transcription	HSMM	muscle
8	chr3:139065000-139104000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:139065200-139089200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:139065200-139093600	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:139065200-139096800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:139065200-139098000	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:139065200-139102000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:139065200-139102200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr3:139065400-139077000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:139065400-139077600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:139065400-139097600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:139065400-139102200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:139065400-139102400	Strong transcription	Duodenum Mucosa	Duodenum
20	chr3:139065400-139102600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:139065400-139102600	Strong transcription	Osteobl	bone
22	chr3:139065400-139103600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr3:139065400-139103800	Strong transcription	Fetal Thymus	thymus
24	chr3:139065600-139077400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:139065600-139079600	Strong transcription	Fetal Lung	lung
26	chr3:139065600-139100200	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr3:139065600-139101800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:139065600-139102400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:139065600-139102400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:139065600-139102400	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr3:139065600-139103600	Strong transcription	HUVEC	blood vessel
32	chr3:139065600-139103600	Strong transcription	NH-A	brain
33	chr3:139065600-139103800	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr3:139065600-139103800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr3:139065800-139078000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:139065800-139080800	Strong transcription	Brain Germinal Matrix	brain
37	chr3:139065800-139081000	Strong transcription	Fetal Brain Female	brain
38	chr3:139065800-139095000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:139065800-139096200	Strong transcription	Liver	Liver
40	chr3:139065800-139098200	Strong transcription	Primary hematopoietic stem cells	blood
41	chr3:139065800-139098200	Strong transcription	HMEC	breast
42	chr3:139065800-139101600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:139065800-139101600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr3:139065800-139102400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:139065800-139102400	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr3:139065800-139102600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:139065800-139102800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:139065800-139103200	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr3:139065800-139103600	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:139065800-139104400	Strong transcription	Dnd41	blood

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