Variant report

Variant	rs967608
Chromosome Location	chr3:100011805-100011806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1036770	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936157	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11915985	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1214369	0.87[EUR][1000 genomes]
rs1214371	0.84[ASN][1000 genomes]
rs1214372	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs1214373	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs12696084	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs13070392	0.88[CEU][hapmap]
rs1609481	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2028494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2029162	0.95[CHB][hapmap]
rs277636	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs277637	0.95[CHB][hapmap]
rs277652	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs277654	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs277655	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs3772698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384528	0.84[ASN][1000 genomes]
rs4345098	0.82[ASN][1000 genomes]
rs4552390	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928118	0.95[CHB][hapmap]
rs4928119	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4928169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62281675	0.85[EUR][1000 genomes]
rs6763594	0.85[EUR][1000 genomes]
rs6802765	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6804963	0.95[CHB][hapmap]
rs6808175	0.84[EUR][1000 genomes]
rs7427443	0.84[EUR][1000 genomes]
rs7618677	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs7630257	0.85[EUR][1000 genomes]
rs7637157	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs7638503	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs931332	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9863237	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9863738	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs9880795	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs9882337	0.84[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs967608	TBC1D23	cis	Muscle Skeletal	GTEx

Chromatin state (count:120 , 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	chr3:99981200-100030800	Weak transcription	Fetal Heart	heart
4	chr3:99986600-100024800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:99988800-100013800	Weak transcription	Fetal Brain Male	brain
6	chr3:99989000-100025000	Weak transcription	Fetal Brain Female	brain
7	chr3:99990600-100030600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:99990800-100021400	Weak transcription	Psoas Muscle	Psoas
9	chr3:99992400-100017600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:99994200-100014200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:99994400-100040800	Weak transcription	Esophagus	oesophagus
12	chr3:99995400-100019000	Weak transcription	Colonic Mucosa	Colon
13	chr3:99996000-100012400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:99996000-100052800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:99996000-100053000	Weak transcription	Small Intestine	intestine
16	chr3:99996400-100025600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:99996800-100016800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:99997200-100017800	Weak transcription	Brain Angular Gyrus	brain
19	chr3:99997600-100017000	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:99997800-100031800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:99998000-100013600	Weak transcription	Fetal Kidney	kidney
22	chr3:99998200-100013400	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:99998200-100016200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:99998400-100028000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:99998600-100015400	Strong transcription	Osteobl	bone
26	chr3:99998600-100026400	Strong transcription	HSMM	muscle
27	chr3:99998600-100033800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:99998800-100012000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:99998800-100019800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:99998800-100021800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr3:99998800-100026600	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:99999000-100012600	Strong transcription	Duodenum Mucosa	Duodenum
33	chr3:99999200-100012800	Strong transcription	Placenta	Placenta
34	chr3:99999800-100012600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr3:100000400-100012600	Strong transcription	Fetal Thymus	thymus
36	chr3:100000800-100015800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:100001000-100014200	Weak transcription	Stomach Mucosa	stomach
38	chr3:100001600-100014000	Weak transcription	GM12878-XiMat	blood
39	chr3:100001800-100014200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr3:100002200-100013600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:100002400-100018400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:100003400-100015000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:100004800-100012400	Strong transcription	Fetal Intestine Large	intestine
44	chr3:100005200-100013600	Weak transcription	HepG2	liver
45	chr3:100005200-100021600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr3:100005800-100012000	Strong transcription	Brain Germinal Matrix	brain
47	chr3:100005800-100015000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:100006000-100018000	Weak transcription	Ovary	ovary
49	chr3:100006000-100019800	Weak transcription	Hela-S3	cervix
50	chr3:100006600-100012600	Strong transcription	Duodenum Smooth Muscle	Duodenum

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