Variant report

Variant	rs1291
Chromosome Location	chr19:38229378-38229379
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10048511	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10402671	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10403173	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs10404031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs10404567	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs10406379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs10408619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10409402	0.84[ASN][1000 genomes]
rs10409487	0.84[ASN][1000 genomes]
rs10409605	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10415548	0.88[CEU][hapmap]
rs10417576	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10420746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10853710	0.81[AFR][1000 genomes]
rs11083432	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs11083433	0.82[LWK][hapmap];1.00[YRI][hapmap]
rs1119229	0.88[CEU][hapmap]
rs11673023	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12974225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12979640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs1531549	0.83[EUR][1000 genomes]
rs1564208	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs16958861	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16958863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16975299	0.92[YRI][hapmap]
rs171376	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17246792	0.96[YRI][hapmap]
rs1974714	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1975937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2075281	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2075284	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2287229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2291002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs241932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs241933	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs241950	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2909085	0.87[ASN][1000 genomes]
rs2909088	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs2909093	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2909098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2909100	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2909102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2909105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2909109	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs2927739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2927740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2927742	0.81[ASN][1000 genomes]
rs2927746	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2927747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2972430	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2972434	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972445	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972446	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972448	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs2972458	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3095724	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3095726	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3101746	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3101747	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3112433	0.82[ASN][1000 genomes]
rs3112434	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35863684	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3786869	0.87[CEU][hapmap]
rs3829688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs4239516	0.87[CEU][hapmap]
rs4802024	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap]
rs4802029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4802135	0.86[CHB][hapmap]
rs4803262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4803509	0.84[ASN][1000 genomes]
rs4803524	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs4803551	0.88[CEU][hapmap]
rs4803573	0.88[CEU][hapmap]
rs56151076	0.87[ASN][1000 genomes]
rs56317671	0.81[EUR][1000 genomes]
rs6508736	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs6508742	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs705494	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[TSI][hapmap]
rs705495	0.88[CEU][hapmap]
rs7249622	0.92[YRI][hapmap]
rs7250409	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[TSI][hapmap]
rs7253081	0.96[YRI][hapmap]
rs8102579	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[TSI][hapmap]
rs8103633	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103647	0.83[EUR][1000 genomes]
rs8110284	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs8112706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8113521	0.88[CEU][hapmap]
rs856300	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs856304	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9304569	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs954504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs958305	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs968073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9749368	0.85[EUR][1000 genomes];0.85[ASN][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	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
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1291	ZNF571	cis	multi-tissue	Pritchard
rs1291	PHLDB3	cis	parietal	SCAN
rs1291	HIPK4	cis	cerebellum	SCAN
rs1291	CBLC	cis	parietal	SCAN
rs1291	PHLDB3	cis	cerebellum	SCAN
rs1291	DMPK	cis	parietal	SCAN
rs1291	PAFAH1B3	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38210800-38229400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:38211000-38229400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:38211000-38229400	Weak transcription	Brain Germinal Matrix	brain
4	chr19:38211000-38229400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr19:38211000-38230200	Weak transcription	Hela-S3	cervix
6	chr19:38221200-38241800	ZNF genes & repeats	Liver	Liver
7	chr19:38224000-38229400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:38224600-38241600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:38225200-38232400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr19:38225200-38232400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
11	chr19:38225200-38232400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
12	chr19:38225200-38232400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
13	chr19:38225200-38232400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
14	chr19:38225200-38237200	ZNF genes & repeats	Adipose Nuclei	Adipose
15	chr19:38225400-38231600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:38225400-38232400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:38225400-38232400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
18	chr19:38226000-38232200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr19:38226200-38232200	ZNF genes & repeats	Primary T cells from cord blood	blood
20	chr19:38226200-38232400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr19:38227200-38231600	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
22	chr19:38227400-38231000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
23	chr19:38227400-38232400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:38227400-38233600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
25	chr19:38227600-38230800	ZNF genes & repeats	Brain Hippocampus Middle	brain
26	chr19:38227600-38231600	ZNF genes & repeats	Ovary	ovary
27	chr19:38227800-38229600	ZNF genes & repeats	Pancreas	Pancrea
28	chr19:38228200-38229400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:38228200-38229800	Weak transcription	Fetal Brain Male	brain
30	chr19:38228200-38231400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr19:38228200-38231800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:38228200-38232000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
33	chr19:38228400-38232200	ZNF genes & repeats	Colon Smooth Muscle	Colon
34	chr19:38228400-38232400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr19:38228400-38232400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
36	chr19:38228400-38232400	ZNF genes & repeats	Fetal Muscle Leg	muscle
37	chr19:38228600-38230400	Weak transcription	Fetal Stomach	stomach
38	chr19:38228600-38231000	ZNF genes & repeats	Brain Substantia Nigra	brain
39	chr19:38228600-38231400	ZNF genes & repeats	Rectal Smooth Muscle	rectum
40	chr19:38228800-38230400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:38229000-38230000	Weak transcription	Fetal Thymus	thymus
42	chr19:38229000-38231200	ZNF genes & repeats	Psoas Muscle	Psoas
43	chr19:38229000-38231600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr19:38229000-38238000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
45	chr19:38229200-38229400	Weak transcription	Fetal Heart	heart
46	chr19:38229200-38229800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
47	chr19:38229200-38230400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
48	chr19:38229200-38230400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr19:38229200-38230400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
50	chr19:38229200-38230600	ZNF genes & repeats	Right Ventricle	heart

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