Variant report

Variant	rs8039438
Chromosome Location	chr15:43132840-43132841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10220713	0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10220718	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10220875	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10438302	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070381	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324135	0.81[JPT][hapmap]
rs12324838	1.00[EUR][1000 genomes]
rs12594858	1.00[EUR][1000 genomes]
rs1317628	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs13380301	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs16957043	0.81[JPT][hapmap]
rs16957052	1.00[MEX][hapmap]
rs16957125	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[ASN][1000 genomes]
rs16957138	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs16957178	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16957187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16957224	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1915243	0.90[JPT][hapmap]
rs34348991	0.84[ASN][1000 genomes]
rs56894749	0.96[ASN][1000 genomes]
rs58506324	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58754188	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58756153	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60752181	0.85[ASN][1000 genomes]
rs60753136	1.00[EUR][1000 genomes]
rs60789298	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60807675	0.84[ASN][1000 genomes]
rs60832391	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60881935	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61682243	0.96[ASN][1000 genomes]
rs6493058	1.00[MEX][hapmap]
rs7162040	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs7163324	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs7164041	0.92[ASW][hapmap]
rs7165249	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs7174661	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7177501	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7181448	1.00[MEX][hapmap]
rs8023743	0.81[JPT][hapmap]
rs8027319	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs8032994	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8039217	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs8039346	1.00[JPT][hapmap]
rs8043143	0.81[JPT][hapmap]
rs9806313	0.92[ASW][hapmap];0.85[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv977054	chr15:43015821-43171355	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1050128	chr15:43056145-43262736	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv542368	chr15:43056145-43262736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv904134	chr15:43097652-43357406	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8039438	CCNDBP1	cis	multi-tissue	Pritchard

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43054800-43146000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr15:43063400-43136200	Weak transcription	Psoas Muscle	Psoas
3	chr15:43064800-43150800	Weak transcription	HSMM	muscle
4	chr15:43067400-43147200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:43075200-43143800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr15:43075400-43135800	Weak transcription	HSMMtube	muscle
7	chr15:43075600-43150800	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:43075800-43134800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:43075800-43159200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:43089800-43165200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:43091800-43135400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:43094400-43163800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr15:43094600-43150800	Weak transcription	Aorta	Aorta
14	chr15:43095000-43165000	Weak transcription	Spleen	Spleen
15	chr15:43095600-43136000	Weak transcription	Fetal Brain Female	brain
16	chr15:43095800-43139000	Weak transcription	Esophagus	oesophagus
17	chr15:43096000-43133800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr15:43096000-43135600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:43096000-43136000	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:43096200-43136000	Weak transcription	Lung	lung
21	chr15:43103000-43133400	Weak transcription	Brain Substantia Nigra	brain
22	chr15:43103000-43134600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr15:43103000-43136000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr15:43103000-43165400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:43103200-43138400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:43103400-43133800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr15:43103400-43136000	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:43103400-43173200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr15:43106000-43136000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr15:43106200-43142000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:43107400-43134400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:43108200-43136200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr15:43110800-43136000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:43112600-43138000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr15:43114800-43172000	Weak transcription	Pancreas	Pancrea
36	chr15:43118200-43139200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:43118400-43144400	Weak transcription	Gastric	stomach
38	chr15:43119200-43136000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:43119600-43136200	Weak transcription	Fetal Lung	lung
40	chr15:43119600-43168200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr15:43119600-43172600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr15:43119800-43163200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr15:43119800-43170200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr15:43120000-43136000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr15:43120000-43142000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr15:43120000-43151000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr15:43120200-43135800	Weak transcription	Fetal Intestine Large	intestine
48	chr15:43120600-43141800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr15:43122000-43136000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:43125200-43136000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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