Variant report

Variant	rs9880795
Chromosome Location	chr3:99995930-99995931
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99982526..99986006-chr3:99993690..99996529,5	K562	blood:
2	chr3:99995357..99997620-chr3:99997691..100000135,2	K562	blood:
3	chr3:99987793..99990529-chr3:99994946..99997286,3	K562	blood:
4	chr3:99993830..99996314-chr3:100052035..100053568,2	K562	blood:

Variant related genes	Relation type
ENSG00000036054	Chromatin interaction
ENSG00000114021	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1036770	0.85[EUR][1000 genomes]
rs10936157	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs11915985	0.85[EUR][1000 genomes]
rs1214369	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1214372	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1214373	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12696064	1.00[ASN][1000 genomes]
rs12696084	0.96[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070392	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1609481	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs2028494	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs2029163	1.00[ASN][1000 genomes]
rs277636	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277652	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277654	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35950794	1.00[ASN][1000 genomes]
rs3772698	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs4552390	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs4928119	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs4928169	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs62281675	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763594	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777265	0.95[ASN][1000 genomes]
rs6802765	0.88[EUR][1000 genomes]
rs6808175	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7427443	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618677	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630257	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637157	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638503	0.88[EUR][1000 genomes]
rs9289985	0.85[JPT][hapmap]
rs931332	0.88[EUR][1000 genomes]
rs967608	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs9854260	0.85[JPT][hapmap]
rs9860290	0.85[JPT][hapmap]
rs9863738	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875878	0.85[JPT][hapmap]
rs9882337	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:3 , 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
3	nsv869690	chr3:99984442-100054949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9880795	TBC1D23	cis	Muscle Skeletal	GTEx
rs9880795	TBC1D23	cis	Heart Left Ventricle	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99980600-100037200	Weak transcription	Spleen	Spleen
2	chr3:99980600-100053200	Weak transcription	Gastric	stomach
3	chr3:99981000-99996400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:99981200-99997800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr3:99981200-99998400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr3:99981200-99998600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:99981200-99998600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:99981200-100004800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:99981200-100030800	Weak transcription	Fetal Heart	heart
10	chr3:99981400-99998400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr3:99981400-100004400	Weak transcription	Lung	lung
12	chr3:99982400-100005400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:99982600-99998800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:99982800-100001400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:99983200-99999600	Weak transcription	Fetal Intestine Large	intestine
16	chr3:99983200-100010000	Weak transcription	Pancreas	Pancrea
17	chr3:99983400-99999400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:99984200-99998200	Weak transcription	Primary T cells from cord blood	blood
19	chr3:99984200-99998800	Weak transcription	Fetal Intestine Small	intestine
20	chr3:99984200-99999000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:99984200-99999400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:99984200-100010000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:99984200-100011000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:99985800-99997800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:99985800-99998000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:99986600-100024800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr3:99988200-99999200	Weak transcription	Liver	Liver
28	chr3:99988600-99996000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:99988800-100013800	Weak transcription	Fetal Brain Male	brain
30	chr3:99989000-99997200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:99989000-99998600	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:99989000-99999400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:99989000-100002000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:99989000-100005800	Weak transcription	Thymus	Thymus
35	chr3:99989000-100007600	Weak transcription	HUVEC	blood vessel
36	chr3:99989000-100025000	Weak transcription	Fetal Brain Female	brain
37	chr3:99989200-99998800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:99989200-99999400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:99989200-100000400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:99989400-99998200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:99989400-99998800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:99989400-100000400	Weak transcription	Adipose Nuclei	Adipose
43	chr3:99990200-99997800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:99990400-99996600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:99990400-99998600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:99990400-99998800	Weak transcription	Fetal Stomach	stomach
47	chr3:99990400-99999000	Weak transcription	NH-A	brain
48	chr3:99990400-100005000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:99990400-100006000	Weak transcription	HSMMtube	muscle
50	chr3:99990600-99998800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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