Variant report

Variant	rs332860
Chromosome Location	chr19:38657130-38657131
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38655531..38657152-chr19:38659489..38661396,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10460171	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11083447	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12460188	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12462587	0.83[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs12975576	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12984016	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12984864	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12985707	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1545039	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1962866	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2004981	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2010234	0.96[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs2016074	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2116862	0.82[EUR][1000 genomes]
rs2304132	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2569517	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs332841	0.92[CEU][hapmap];0.84[GIH][hapmap]
rs332845	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs332846	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs332857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs332859	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs332861	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs332862	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs332863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34646932	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35467693	0.82[EUR][1000 genomes]
rs35469521	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35972455	0.83[ASN][1000 genomes]
rs3852910	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3852911	0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4802248	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803805	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4803808	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67910767	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71337549	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7253312	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7253633	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8100956	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8107385	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs855617	0.81[EUR][1000 genomes];0.83[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	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
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911657	chr19:38655449-38753786	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs332860	ERF	cis	cerebellum	SCAN
rs332860	MARK4	cis	cerebellum	SCAN
rs332860	EGLN2	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38638200-38667200	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr19:38644000-38659200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr19:38645600-38660800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:38646000-38661000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr19:38651400-38658400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:38652400-38657400	Strong transcription	Brain Angular Gyrus	brain
7	chr19:38653400-38657800	Strong transcription	Colonic Mucosa	Colon
8	chr19:38653400-38658400	Strong transcription	Rectal Smooth Muscle	rectum
9	chr19:38653400-38658800	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr19:38653400-38659600	Strong transcription	Primary B cells from cord blood	blood
11	chr19:38653400-38659600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr19:38653400-38660400	Strong transcription	GM12878-XiMat	blood
13	chr19:38653400-38661400	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr19:38653400-38663400	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr19:38653600-38657400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:38653600-38657600	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr19:38653600-38657600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr19:38653600-38657600	Strong transcription	Left Ventricle	heart
19	chr19:38653600-38657600	Strong transcription	NH-A	brain
20	chr19:38653600-38658400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr19:38653600-38658600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:38653600-38658600	Strong transcription	Ovary	ovary
23	chr19:38653600-38659000	Weak transcription	Fetal Heart	heart
24	chr19:38653600-38659200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr19:38653600-38659600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr19:38653600-38659800	Weak transcription	Fetal Brain Male	brain
27	chr19:38653600-38660200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:38653600-38660200	Strong transcription	Primary T cells from cord blood	blood
29	chr19:38653600-38660400	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr19:38653600-38661200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:38653600-38661200	Strong transcription	Duodenum Mucosa	Duodenum
32	chr19:38653600-38661400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr19:38653600-38661400	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr19:38653600-38661600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:38653600-38663200	Strong transcription	Gastric	stomach
36	chr19:38653600-38663400	Weak transcription	HUVEC	blood vessel
37	chr19:38653600-38663800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr19:38653600-38663800	Strong transcription	Fetal Intestine Large	intestine
39	chr19:38653600-38665200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:38653600-38668600	Strong transcription	Primary B cells from peripheral blood	blood
41	chr19:38653600-38696400	Weak transcription	Small Intestine	intestine
42	chr19:38653800-38657800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr19:38653800-38658200	Weak transcription	Fetal Kidney	kidney
44	chr19:38653800-38658200	Weak transcription	Fetal Thymus	thymus
45	chr19:38653800-38658600	Strong transcription	Fetal Muscle Leg	muscle
46	chr19:38653800-38658800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr19:38653800-38658800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr19:38653800-38658800	Strong transcription	Lung	lung
49	chr19:38653800-38658800	Strong transcription	Pancreas	Pancrea
50	chr19:38653800-38658800	Strong transcription	Stomach Smooth Muscle	stomach

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