Variant report

Variant	rs2279149
Chromosome Location	chr19:38024367-38024368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs1015848	0.86[EUR][1000 genomes]
rs1015849	0.81[ASW][hapmap];0.93[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs10403173	0.88[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.86[YRI][hapmap]
rs10403582	0.84[EUR][1000 genomes]
rs10404031	0.88[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.86[YRI][hapmap]
rs10404920	0.81[ASW][hapmap];0.93[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]
rs10404945	1.00[CEU][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes]
rs10405064	0.88[ASW][hapmap];0.93[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]
rs10405407	0.93[CEU][hapmap];0.86[TSI][hapmap]
rs10406177	0.93[CEU][hapmap];0.91[TSI][hapmap]
rs10406379	0.88[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.86[YRI][hapmap]
rs10407084	0.81[ASW][hapmap];0.93[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs10408619	0.90[CHB][hapmap]
rs10409204	0.81[ASW][hapmap];0.93[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs10411574	0.94[EUR][1000 genomes]
rs10414904	0.93[CEU][hapmap]
rs10415937	0.93[CEU][hapmap]
rs10417503	0.88[ASW][hapmap];0.93[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]
rs10417844	0.87[CEU][hapmap];0.86[TSI][hapmap]
rs10420722	0.89[EUR][1000 genomes]
rs10420754	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs10422667	0.86[EUR][1000 genomes]
rs10424574	0.88[ASW][hapmap];0.93[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs10426618	0.86[EUR][1000 genomes]
rs11083426	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12972252	0.86[EUR][1000 genomes]
rs12979470	0.82[EUR][1000 genomes]
rs12979640	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs13343471	0.81[ASW][hapmap];0.93[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs13343502	0.81[ASW][hapmap];0.93[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs13345116	0.93[CEU][hapmap]
rs1373991	0.93[CEU][hapmap];0.86[TSI][hapmap]
rs13744	0.88[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.86[YRI][hapmap]
rs1382357	0.93[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs1559229	0.93[CEU][hapmap]
rs1564208	0.88[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap]
rs16958861	0.91[CHB][hapmap];0.82[YRI][hapmap]
rs16958863	0.88[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap]
rs1975937	0.91[CHB][hapmap];0.86[YRI][hapmap]
rs2045908	0.87[EUR][1000 genomes]
rs2081096	0.93[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2112922	0.81[EUR][1000 genomes]
rs2112923	0.93[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs2126977	1.00[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs2279148	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287229	0.82[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap]
rs2291002	0.88[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.86[YRI][hapmap]
rs2291004	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs2303131	0.81[ASW][hapmap];0.93[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs28373708	0.87[EUR][1000 genomes]
rs28538699	0.88[EUR][1000 genomes]
rs28605784	0.85[EUR][1000 genomes]
rs28623164	0.82[EUR][1000 genomes]
rs2891699	0.93[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs2909088	0.88[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap]
rs2909093	0.88[ASW][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap]
rs2909098	0.88[ASW][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap]
rs2909102	0.88[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap]
rs2909105	0.82[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap]
rs2909109	0.88[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap]
rs2927739	0.91[CHB][hapmap]
rs2927740	0.88[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.82[YRI][hapmap]
rs2927747	0.88[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap]
rs2972437	0.88[ASW][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap]
rs2972438	0.88[ASW][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap]
rs2972439	0.88[ASW][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap]
rs2972447	0.91[CHB][hapmap];0.82[YRI][hapmap]
rs2972448	0.88[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap]
rs35540940	0.95[EUR][1000 genomes]
rs35777021	0.84[EUR][1000 genomes]
rs3745765	0.93[CEU][hapmap];0.86[TSI][hapmap]
rs3760825	0.93[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs3829688	0.88[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.86[YRI][hapmap]
rs4417644	0.87[ASW][hapmap];0.93[CEU][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs4452075	0.93[CEU][hapmap];0.86[TSI][hapmap]
rs4801759	0.81[ASW][hapmap];0.93[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs4801803	0.93[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs4802024	0.88[ASW][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.86[YRI][hapmap]
rs4802029	0.90[CHB][hapmap];0.86[YRI][hapmap]
rs4802766	0.90[EUR][1000 genomes]
rs4802889	0.93[EUR][1000 genomes]
rs4803195	0.91[EUR][1000 genomes]
rs4803210	0.88[CEU][hapmap]
rs4803229	0.93[CEU][hapmap];0.86[TSI][hapmap]
rs4803262	0.91[CHB][hapmap];0.86[YRI][hapmap]
rs59224125	0.85[EUR][1000 genomes]
rs6508719	0.93[CEU][hapmap]
rs6508732	1.00[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs6508733	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6508736	0.88[ASW][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.86[YRI][hapmap]
rs713256	0.81[ASW][hapmap];0.93[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]
rs7247259	0.93[CEU][hapmap]
rs7248733	1.00[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs7252099	0.84[EUR][1000 genomes]
rs7252325	0.82[EUR][1000 genomes]
rs7252346	0.93[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs7253091	0.93[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs7253114	1.00[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs7255407	0.82[EUR][1000 genomes]
rs7255785	0.84[EUR][1000 genomes]
rs7255952	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7255972	0.81[ASW][hapmap];0.93[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs7255996	0.84[EUR][1000 genomes]
rs73631095	0.88[EUR][1000 genomes]
rs8106839	0.93[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs8107840	0.87[ASN][1000 genomes]
rs8109038	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]
rs8109632	0.82[EUR][1000 genomes]
rs8111782	0.93[CEU][hapmap]
rs9304566	0.88[ASW][hapmap];0.93[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]
rs954504	0.91[CHB][hapmap];0.86[YRI][hapmap]
rs9676739	0.88[EUR][1000 genomes]
rs9676967	0.82[EUR][1000 genomes]
rs968073	0.82[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap]
rs9917081	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2279149	BLVRB	cis	cerebellum	SCAN
rs2279149	LTBP4	cis	cerebellum	SCAN
rs2279149	HIPK4	cis	parietal	SCAN
rs2279149	PLEKHG2	cis	cerebellum	SCAN
rs2279149	LIPE	cis	cerebellum	SCAN
rs2279149	PAFAH1B3	cis	cerebellum	SCAN
rs2279149	CBLC	cis	parietal	SCAN
rs2279149	EXOSC5	cis	cerebellum	SCAN
rs2279149	PHLDB3	cis	cerebellum	SCAN
rs2279149	DMPK	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37999000-38028800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:38002000-38028800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr19:38008800-38026600	Weak transcription	Fetal Heart	heart
4	chr19:38017400-38028800	ZNF genes & repeats	Adipose Nuclei	Adipose
5	chr19:38018400-38025000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:38021600-38028800	ZNF genes & repeats	Primary T cells from cord blood	blood
7	chr19:38021600-38030200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
8	chr19:38021800-38028800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
9	chr19:38021800-38028800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:38021800-38028800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:38021800-38028800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:38021800-38028800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
13	chr19:38021800-38029800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:38021800-38030000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:38021800-38030800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
16	chr19:38021800-38031600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:38022000-38025000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
18	chr19:38022000-38028400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:38022000-38028800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
20	chr19:38022000-38030600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
21	chr19:38022200-38025600	Strong transcription	Fetal Muscle Leg	muscle
22	chr19:38022200-38025800	ZNF genes & repeats	Pancreas	Pancrea
23	chr19:38022200-38026000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
24	chr19:38022200-38027200	Strong transcription	Right Ventricle	heart
25	chr19:38022200-38028600	ZNF genes & repeats	Primary B cells from cord blood	blood
26	chr19:38022200-38028600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
27	chr19:38022200-38028600	ZNF genes & repeats	Fetal Stomach	stomach
28	chr19:38022200-38028800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
29	chr19:38022200-38028800	ZNF genes & repeats	Esophagus	oesophagus
30	chr19:38022200-38028800	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr19:38022200-38028800	ZNF genes & repeats	Left Ventricle	heart
32	chr19:38022200-38028800	ZNF genes & repeats	Spleen	Spleen
33	chr19:38022200-38029400	ZNF genes & repeats	Aorta	Aorta
34	chr19:38022200-38029600	ZNF genes & repeats	Ovary	ovary
35	chr19:38022200-38030200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:38022200-38037000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
37	chr19:38022400-38024600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:38022400-38025000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
39	chr19:38022400-38025400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr19:38022400-38025800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:38022400-38026000	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:38022400-38026000	Strong transcription	Brain Germinal Matrix	brain
43	chr19:38022400-38026000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:38022400-38026000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
45	chr19:38022400-38026000	ZNF genes & repeats	Gastric	stomach
46	chr19:38022400-38026600	Strong transcription	Fetal Muscle Trunk	muscle
47	chr19:38022400-38027400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr19:38022400-38028000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:38022400-38028600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
50	chr19:38022400-38028600	ZNF genes & repeats	Lung	lung

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