Variant report

Variant	rs9882337
Chromosome Location	chr3:99982150-99982151
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr3:99982056-99982427	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:99982143-99982180	K562	blood:	n/a	n/a
3	GATA1	chr3:99981537-99983408	PBDE	blood:	n/a	chr3:99983275-99983284
4	MAZ	chr3:99981833-99982184	K562	blood:	n/a	n/a
5	CEBPD	chr3:99981697-99982183	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:99979844..99981750-chr3:99981771..99983901,2	MCF-7	breast:
2	chr3:99981876..99985966-chr3:99986124..99992664,8	K562	blood:
3	chr3:99591850..99594536-chr3:99980465..99982700,2	K562	blood:
4	chr3:99571584..99573287-chr3:99980510..99983253,2	K562	blood:
5	chr3:99614799..99616981-chr3:99982145..99984761,2	K562	blood:
6	chr3:99614799..99617137-chr3:99982145..99984761,3	K562	blood:
7	chr3:99981806..99984412-chr3:100006870..100008819,2	K562	blood:

No data

Variant related genes	Relation type
TBC1D23	TF binding region
ENSG00000036054	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1036770	0.84[EUR][1000 genomes]
rs10936157	0.87[EUR][1000 genomes]
rs11915985	0.84[EUR][1000 genomes]
rs1214369	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1214372	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1214373	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12696064	0.82[ASN][1000 genomes]
rs12696084	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13070392	0.89[EUR][1000 genomes]
rs1609481	0.87[EUR][1000 genomes]
rs2028494	0.85[EUR][1000 genomes]
rs2029163	0.82[ASN][1000 genomes]
rs277636	1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs277652	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs277654	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35950794	0.82[ASN][1000 genomes]
rs3772698	0.84[EUR][1000 genomes]
rs4552390	0.84[EUR][1000 genomes]
rs4928119	0.87[EUR][1000 genomes]
rs4928169	0.83[EUR][1000 genomes]
rs62281675	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6763594	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6802765	0.87[EUR][1000 genomes]
rs6808175	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7427443	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7618677	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7630257	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7637157	1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7638503	0.87[EUR][1000 genomes]
rs9289985	1.00[JPT][hapmap]
rs931332	0.87[EUR][1000 genomes]
rs967608	0.84[EUR][1000 genomes]
rs9854260	1.00[JPT][hapmap]
rs9860290	1.00[JPT][hapmap]
rs9863738	1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9875878	1.00[JPT][hapmap]
rs9880795	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9882337	TBC1D23	cis	Heart Left Ventricle	GTEx
rs9882337	TBC1D23	cis	Muscle Skeletal	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99978800-99982400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:99978800-99982400	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr3:99979000-99982400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr3:99979200-99982200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr3:99979200-99982400	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr3:99979200-99982800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:99979600-99982600	Active TSS	K562	blood
8	chr3:99980600-99982200	Weak transcription	Esophagus	oesophagus
9	chr3:99980600-99982200	Weak transcription	Pancreas	Pancrea
10	chr3:99980600-99983200	Enhancers	Small Intestine	intestine
11	chr3:99980600-99983800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr3:99980600-99988600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:99980600-100037200	Weak transcription	Spleen	Spleen
14	chr3:99980600-100053200	Weak transcription	Gastric	stomach
15	chr3:99980800-99982400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:99980800-99982400	Weak transcription	Ovary	ovary
17	chr3:99980800-99983000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr3:99980800-99983200	Enhancers	Brain Substantia Nigra	brain
19	chr3:99980800-99988800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:99981000-99982400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:99981000-99983000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:99981000-99983400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr3:99981000-99983800	Weak transcription	Colonic Mucosa	Colon
24	chr3:99981000-99984400	Enhancers	Liver	Liver
25	chr3:99981000-99990400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:99981000-99996400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:99981200-99982200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:99981200-99982200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:99981200-99982200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:99981200-99982200	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:99981200-99982200	Weak transcription	Primary T cells from cord blood	blood
32	chr3:99981200-99982200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr3:99981200-99982200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:99981200-99982200	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:99981200-99982200	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:99981200-99982200	Weak transcription	Psoas Muscle	Psoas
37	chr3:99981200-99982200	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr3:99981200-99982200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:99981200-99982200	Weak transcription	Hela-S3	cervix
40	chr3:99981200-99982200	Weak transcription	HMEC	breast
41	chr3:99981200-99982200	Weak transcription	NH-A	brain
42	chr3:99981200-99982200	Weak transcription	Osteobl	bone
43	chr3:99981200-99982400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:99981200-99982400	Enhancers	NHEK	skin
45	chr3:99981200-99982600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:99981200-99982600	Weak transcription	Brain Anterior Caudate	brain
47	chr3:99981200-99982600	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr3:99981200-99982600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:99981200-99982800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:99981200-99982800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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