Variant report

Variant	rs12438635
Chromosome Location	chr15:93545934-93545935
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10520716	0.89[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs10520717	0.81[JPT][hapmap]
rs10520718	0.81[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs10520719	0.87[JPT][hapmap]
rs1074512	0.86[ASW][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11630582	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs11634204	0.81[JPT][hapmap]
rs11634207	0.87[JPT][hapmap]
rs11634566	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11857466	0.81[AMR][1000 genomes]
rs11857669	0.80[AMR][1000 genomes]
rs12437674	0.89[CEU][hapmap];0.86[CHB][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs12443243	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs12591124	0.86[ASW][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12592920	0.93[YRI][hapmap];0.83[AMR][1000 genomes]
rs12594991	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12905312	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12906132	0.87[JPT][hapmap]
rs12907579	0.87[JPT][hapmap]
rs12908494	0.80[EUR][1000 genomes]
rs1320819	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs1534779	0.87[JPT][hapmap]
rs17525800	0.87[JPT][hapmap]
rs17610487	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1881835	0.89[CEU][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2033844	0.87[JPT][hapmap]
rs2272457	0.87[JPT][hapmap]
rs2388054	0.84[AFR][1000 genomes]
rs2388055	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs34448107	0.80[AMR][1000 genomes]
rs36032658	0.80[AMR][1000 genomes]
rs3736619	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs3743469	0.87[EUR][1000 genomes]
rs3784785	0.81[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3784786	0.87[JPT][hapmap]
rs3817597	0.81[JPT][hapmap]
rs3826035	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3826036	0.89[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs4327000	0.88[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs4778065	0.86[JPT][hapmap]
rs62023146	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6497009	0.85[EUR][1000 genomes]
rs6497010	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6497011	0.82[CHB][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap]
rs6497013	0.93[ASW][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7164668	0.88[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs7167194	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs7168780	0.85[EUR][1000 genomes]
rs7171151	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7173103	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7174043	0.83[AMR][1000 genomes]
rs7175134	0.80[EUR][1000 genomes]
rs7179863	0.81[AMR][1000 genomes]
rs8024528	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs8035739	0.89[CEU][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs8042395	0.96[MEX][hapmap]
rs9302362	0.96[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
2	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
3	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
4	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv530847	chr15:93444024-93555676	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
6	nsv917347	chr15:93444094-93586814	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12438635	PLIN1	cis	cerebellum	SCAN
rs12438635	KIF7	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93493200-93571000	Strong transcription	Dnd41	blood
2	chr15:93493200-93571200	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr15:93493400-93548000	Strong transcription	Muscle Satellite Cultured Cells	--
4	chr15:93493400-93568600	Strong transcription	Liver	Liver
5	chr15:93493400-93569600	Strong transcription	Placenta	Placenta
6	chr15:93493400-93571000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:93493400-93571000	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr15:93493600-93571400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr15:93493800-93561400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:93493800-93571400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:93494000-93568200	Strong transcription	Fetal Thymus	thymus
12	chr15:93494000-93570400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr15:93494000-93570800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:93494000-93571000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:93494000-93571400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:93504000-93567800	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr15:93505000-93569800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:93506000-93569800	Strong transcription	HepG2	liver
19	chr15:93506400-93561800	Strong transcription	A549	lung
20	chr15:93506400-93569600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr15:93509600-93568000	Strong transcription	Primary B cells from cord blood	blood
22	chr15:93509600-93569600	Strong transcription	NHDF-Ad	bronchial
23	chr15:93509600-93571200	Strong transcription	Fetal Lung	lung
24	chr15:93509600-93571400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr15:93509800-93568600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:93509800-93572000	Strong transcription	Fetal Intestine Large	intestine
27	chr15:93512800-93560200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr15:93512800-93567800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:93512800-93567800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:93512800-93568000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:93513800-93560000	Strong transcription	Fetal Kidney	kidney
32	chr15:93514200-93561000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:93514200-93570800	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr15:93515000-93561000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr15:93519200-93548600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:93521200-93568200	Strong transcription	Primary hematopoietic stem cells	blood
37	chr15:93521600-93548000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr15:93521600-93568000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr15:93521800-93569400	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:93522800-93547800	Strong transcription	Osteobl	bone
41	chr15:93522800-93563200	Strong transcription	GM12878-XiMat	blood
42	chr15:93523000-93570600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:93524600-93548800	Strong transcription	Colon Smooth Muscle	Colon
44	chr15:93525600-93563600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr15:93525600-93570600	Strong transcription	NH-A	brain
46	chr15:93525800-93560400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr15:93525800-93567000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:93525800-93568600	Strong transcription	HUVEC	blood vessel
49	chr15:93526000-93570400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:93526200-93546000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood

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