Variant report

Variant	rs8109038
Chromosome Location	chr19:38015709-38015710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1015848	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1015849	0.88[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10403173	0.82[ASW][hapmap]
rs10403582	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10404031	0.82[ASW][hapmap]
rs10404920	0.87[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs10404945	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10405064	0.81[ASW][hapmap];0.93[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs10405407	0.93[CEU][hapmap];0.84[JPT][hapmap];0.86[TSI][hapmap]
rs10406177	0.93[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs10406379	0.82[ASW][hapmap]
rs10407084	0.88[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10409204	0.87[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10411574	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10413602	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10414904	0.93[CEU][hapmap];0.84[JPT][hapmap]
rs10415937	0.93[CEU][hapmap];0.84[JPT][hapmap]
rs10417503	0.81[ASW][hapmap];0.93[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs10417844	0.87[CEU][hapmap];0.80[JPT][hapmap];0.86[TSI][hapmap]
rs10420430	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10420722	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10420754	0.93[CEU][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs10422074	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10422667	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10424574	0.81[ASW][hapmap];0.93[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs10426618	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11083426	0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs12972252	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12979470	0.83[EUR][1000 genomes]
rs12981532	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13343471	0.87[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13343502	0.88[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13345116	0.93[CEU][hapmap];0.84[JPT][hapmap]
rs1373991	0.93[CEU][hapmap];0.84[JPT][hapmap];0.86[TSI][hapmap]
rs13744	0.82[ASW][hapmap]
rs1382357	0.93[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs1559229	0.93[CEU][hapmap];0.94[JPT][hapmap]
rs1564208	0.82[ASW][hapmap]
rs16958863	0.82[ASW][hapmap];0.81[LWK][hapmap]
rs2045908	0.89[EUR][1000 genomes]
rs2081096	0.93[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs2112922	0.82[EUR][1000 genomes]
rs2112923	0.93[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2126977	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2279148	1.00[CEU][hapmap];0.86[YRI][hapmap];0.98[EUR][1000 genomes]
rs2279149	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2287229	0.81[LWK][hapmap]
rs2291002	0.82[ASW][hapmap]
rs2291004	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2303131	0.87[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28373708	0.89[EUR][1000 genomes]
rs28538699	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28605784	0.87[EUR][1000 genomes]
rs28623164	0.83[EUR][1000 genomes]
rs2891699	0.93[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs2909088	0.82[ASW][hapmap];0.81[LWK][hapmap]
rs2909093	0.82[ASW][hapmap];0.81[LWK][hapmap]
rs2909098	0.82[ASW][hapmap];0.81[LWK][hapmap]
rs2909102	0.82[ASW][hapmap];0.81[LWK][hapmap]
rs2909105	0.81[LWK][hapmap]
rs2909109	0.82[ASW][hapmap];0.81[LWK][hapmap]
rs2927740	0.82[ASW][hapmap]
rs2927747	0.82[ASW][hapmap];0.81[LWK][hapmap]
rs2972437	0.82[ASW][hapmap];0.81[LWK][hapmap]
rs2972438	0.82[ASW][hapmap];0.81[LWK][hapmap]
rs2972439	0.82[ASW][hapmap];0.81[LWK][hapmap]
rs2972448	0.82[ASW][hapmap];0.81[LWK][hapmap]
rs35540940	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35777021	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3745765	0.93[CEU][hapmap];0.84[JPT][hapmap];0.86[TSI][hapmap]
rs3760825	0.93[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs3829688	0.82[ASW][hapmap]
rs4417644	0.93[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap]
rs4452075	0.93[CEU][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap]
rs4801759	0.87[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4801803	0.94[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4802024	0.82[ASW][hapmap]
rs4802766	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802889	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803195	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4803210	0.88[CEU][hapmap]
rs4803229	0.93[CEU][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap]
rs59224125	0.87[EUR][1000 genomes]
rs6508719	0.93[CEU][hapmap];0.94[JPT][hapmap]
rs6508732	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs6508733	1.00[CEU][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes]
rs6508736	0.82[ASW][hapmap]
rs713256	0.87[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap]
rs7246993	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7247259	0.93[CEU][hapmap];0.84[JPT][hapmap]
rs7248733	1.00[CEU][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs7252099	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7252325	0.83[EUR][1000 genomes]
rs7252346	0.93[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs7253091	0.93[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs7253114	1.00[CEU][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs7255140	0.80[AMR][1000 genomes]
rs7255407	0.83[EUR][1000 genomes]
rs7255785	0.85[EUR][1000 genomes]
rs7255952	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7255972	0.88[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7255996	0.85[EUR][1000 genomes]
rs7256130	0.81[EUR][1000 genomes]
rs7257672	0.93[CEU][hapmap];0.80[JPT][hapmap]
rs7258692	0.93[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap]
rs73631095	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8106839	0.93[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8109632	0.83[EUR][1000 genomes]
rs8111782	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs8112610	0.81[EUR][1000 genomes]
rs9304566	0.81[ASW][hapmap];0.93[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs9676739	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9676967	0.83[EUR][1000 genomes]
rs968073	0.81[LWK][hapmap]
rs9917081	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1056753	chr19:37963714-38015943	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs8109038	MEGF8	cis	cerebellum	SCAN
rs8109038	HIPK4	cis	parietal	SCAN
rs8109038	PLEKHG2	cis	cerebellum	SCAN
rs8109038	LTBP4	cis	cerebellum	SCAN
rs8109038	FAM98C	cis	cerebellum	SCAN
rs8109038	BLVRB	cis	cerebellum	SCAN
rs8109038	PHLDB3	cis	cerebellum	SCAN
rs8109038	PAFAH1B3	cis	cerebellum	SCAN
rs8109038	DMPK	cis	parietal	SCAN
rs8109038	EXOSC5	cis	cerebellum	SCAN
rs8109038	LIPE	cis	cerebellum	SCAN
rs8109038	CBLC	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37998800-38021000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr19:37998800-38022600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:37999000-38028800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:37999200-38018400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:38002000-38028800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr19:38006000-38020800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:38008800-38026600	Weak transcription	Fetal Heart	heart
8	chr19:38009400-38020000	ZNF genes & repeats	Fetal Intestine Small	intestine
9	chr19:38010600-38018400	Strong transcription	Fetal Brain Female	brain
10	chr19:38010600-38020600	Strong transcription	Fetal Muscle Leg	muscle
11	chr19:38010800-38020400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
12	chr19:38010800-38020800	Strong transcription	Brain Anterior Caudate	brain
13	chr19:38011000-38020800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr19:38011600-38023600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr19:38011800-38016600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:38012800-38020800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr19:38013000-38015800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:38013000-38015800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:38013000-38016000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr19:38013000-38017600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
21	chr19:38013000-38017800	ZNF genes & repeats	Ovary	ovary
22	chr19:38013200-38015800	ZNF genes & repeats	Aorta	Aorta
23	chr19:38013200-38015800	ZNF genes & repeats	Left Ventricle	heart
24	chr19:38013200-38016200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
25	chr19:38013200-38018000	ZNF genes & repeats	Fetal Stomach	stomach
26	chr19:38013200-38019600	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr19:38013200-38020400	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr19:38013200-38020800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:38013200-38020800	Strong transcription	Brain Cingulate Gyrus	brain
30	chr19:38013400-38015800	Strong transcription	Fetal Intestine Large	intestine
31	chr19:38013400-38015800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
32	chr19:38013400-38016000	ZNF genes & repeats	Primary T cells from cord blood	blood
33	chr19:38013400-38016000	Strong transcription	Brain Substantia Nigra	brain
34	chr19:38013400-38016000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
35	chr19:38013400-38016000	ZNF genes & repeats	Psoas Muscle	Psoas
36	chr19:38013400-38016200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
37	chr19:38013400-38017000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr19:38013400-38017600	Strong transcription	Brain Angular Gyrus	brain
39	chr19:38013400-38017800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
40	chr19:38013400-38018200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:38013400-38020600	ZNF genes & repeats	Liver	Liver
42	chr19:38013400-38020800	Strong transcription	Brain Germinal Matrix	brain
43	chr19:38013400-38020800	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr19:38013600-38016000	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr19:38013600-38016000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr19:38013800-38015800	Strong transcription	Fetal Kidney	kidney
47	chr19:38013800-38015800	Strong transcription	Stomach Smooth Muscle	stomach
48	chr19:38013800-38018000	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr19:38013800-38019200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:38014000-38016600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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