Variant report

Variant	rs9836756
Chromosome Location	chr3:49822909-49822910
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49759986..49763114-chr3:49822374..49825754,4	MCF-7	breast:
2	chr3:49822569..49826385-chr3:49827149..49830694,4	MCF-7	breast:
3	chr3:49737567..49739735-chr3:49821150..49823977,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164068	Chromatin interaction
ENSG00000173540	Chromatin interaction
ENSG00000187492	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11130217	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709734	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11720705	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12715437	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13091525	1.00[ASN][1000 genomes]
rs13097720	1.00[ASN][1000 genomes]
rs1491985	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17304079	1.00[ASN][1000 genomes]
rs1799844	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996663	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1996664	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28535523	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3020779	0.81[EUR][1000 genomes]
rs35012435	1.00[ASN][1000 genomes]
rs35129566	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375092	1.00[ASN][1000 genomes]
rs35491931	1.00[ASN][1000 genomes]
rs35849525	1.00[ASN][1000 genomes]
rs55997059	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58339610	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59357103	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59684465	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61557789	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62260663	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260720	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260723	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62260755	1.00[ASN][1000 genomes]
rs62262061	1.00[ASN][1000 genomes]
rs62262106	1.00[ASN][1000 genomes]
rs62262118	1.00[ASN][1000 genomes]
rs62262722	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262730	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787892	1.00[ASN][1000 genomes]
rs6790568	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6804970	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809879	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71326904	1.00[ASN][1000 genomes]
rs7613603	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615318	1.00[ASN][1000 genomes]
rs7620848	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621797	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628207	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7635601	1.00[ASN][1000 genomes]
rs7637711	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649428	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829155	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835157	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851651	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870755	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870858	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9836756	AMT	cis	Thyroid	GTEx
rs9836756	RNF123	cis	Artery Tibial	GTEx
rs9836756	AMT	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49775800-49823000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:49786000-49823000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:49818200-49823200	Weak transcription	Gastric	stomach
4	chr3:49819200-49823000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:49819200-49823000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:49819200-49823000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:49819400-49823000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:49819400-49823200	Weak transcription	Aorta	Aorta
9	chr3:49820200-49823200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:49821800-49823000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:49821800-49823000	Enhancers	Fetal Heart	heart
12	chr3:49821800-49823200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:49822000-49823000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:49822000-49823000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:49822200-49823000	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr3:49822400-49823000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:49822400-49823000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:49822400-49823000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr3:49822400-49823000	Enhancers	Liver	Liver
20	chr3:49822400-49823000	Flanking Active TSS	Fetal Brain Female	brain
21	chr3:49822400-49823000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
22	chr3:49822400-49823000	Enhancers	Fetal Kidney	kidney
23	chr3:49822400-49823000	Enhancers	Stomach Mucosa	stomach
24	chr3:49822400-49823000	Flanking Active TSS	Thymus	Thymus
25	chr3:49822400-49823000	Enhancers	Spleen	Spleen
26	chr3:49822400-49823200	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr3:49822400-49823200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr3:49822400-49823200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr3:49822400-49823200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr3:49822400-49823200	Transcr. at gene 5' and 3'	Fetal Lung	lung
31	chr3:49822400-49823200	Enhancers	Small Intestine	intestine
32	chr3:49822400-49823200	Flanking Active TSS	Hela-S3	cervix
33	chr3:49822400-49823200	Flanking Active TSS	NH-A	brain
34	chr3:49822400-49823400	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr3:49822400-49823400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr3:49822400-49823400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:49822400-49823400	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr3:49822400-49823400	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr3:49822400-49823400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr3:49822400-49823400	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr3:49822400-49823600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr3:49822400-49823600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:49822400-49823600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:49822400-49823600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr3:49822400-49824200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:49822400-49824400	Active TSS	Ovary	ovary
47	chr3:49822400-49824600	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr3:49822600-49823000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:49822600-49823000	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr3:49822600-49823000	Flanking Active TSS	Colonic Mucosa	Colon

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