Variant report

Variant	rs12151335
Chromosome Location	chr19:40841508-40841509
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11083554	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12459567	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12460555	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs12460615	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12977474	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12985477	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16974196	0.86[JPT][hapmap]
rs1962639	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1991460	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304186	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs2368575	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33933140	0.89[CEU][hapmap];0.91[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs34894858	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs35562135	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3745195	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4479364	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4490097	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4502340	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4524046	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802072	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802076	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4803324	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803325	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803326	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803327	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803328	0.85[ASN][1000 genomes]
rs55710016	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57158010	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58502633	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59263025	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7259273	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7259541	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs73046335	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7507651	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7508513	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8110323	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs890773	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs892117	0.86[CHB][hapmap];0.86[JPT][hapmap]

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	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12151335	ERCC1	cis	parietal	SCAN
rs12151335	TMEM91	cis	parietal	SCAN
rs12151335	PLAUR	cis	cerebellum	SCAN
rs12151335	SLC1A5	cis	parietal	SCAN
rs12151335	DMRTC2	cis	parietal	SCAN
rs12151335	VASP	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40820800-40848400	Strong transcription	Dnd41	blood
2	chr19:40821400-40846000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr19:40822000-40842400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:40822000-40843400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr19:40822000-40851000	Strong transcription	Fetal Stomach	stomach
6	chr19:40822200-40842400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:40822200-40842600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:40822200-40843200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:40822200-40845400	Strong transcription	Fetal Muscle Leg	muscle
10	chr19:40822400-40846200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr19:40823400-40842400	Strong transcription	Fetal Brain Female	brain
12	chr19:40823400-40845400	Strong transcription	Thymus	Thymus
13	chr19:40824000-40842200	Strong transcription	Liver	Liver
14	chr19:40824000-40842400	Strong transcription	Brain Germinal Matrix	brain
15	chr19:40824000-40842600	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr19:40824200-40846400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:40824200-40848600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr19:40824200-40849600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr19:40824400-40843000	Strong transcription	Fetal Thymus	thymus
20	chr19:40825200-40842800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:40825400-40842600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr19:40825600-40842200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:40825600-40842400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:40825800-40841600	Strong transcription	Right Ventricle	heart
25	chr19:40825800-40842200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr19:40825800-40842200	Strong transcription	Adipose Nuclei	Adipose
27	chr19:40825800-40842400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:40825800-40842400	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr19:40825800-40842400	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr19:40825800-40842600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr19:40825800-40842600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr19:40825800-40845400	Strong transcription	Stomach Smooth Muscle	stomach
33	chr19:40826000-40842200	Strong transcription	Gastric	stomach
34	chr19:40826000-40842400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:40826000-40842400	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr19:40826000-40842400	Strong transcription	Fetal Intestine Large	intestine
37	chr19:40826000-40842400	Strong transcription	Left Ventricle	heart
38	chr19:40826000-40842400	Strong transcription	Ovary	ovary
39	chr19:40826400-40842200	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr19:40826400-40842400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr19:40826400-40843000	Strong transcription	Primary T cells from cord blood	blood
42	chr19:40826400-40847400	Weak transcription	Right Atrium	heart
43	chr19:40826600-40842000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:40826600-40842400	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr19:40826600-40842800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr19:40826600-40853000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr19:40826800-40842200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr19:40826800-40842400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr19:40826800-40842800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:40827600-40845000	Strong transcription	GM12878-XiMat	blood

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