Variant report

Variant	rs2290386
Chromosome Location	chr7:47852837-47852838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11765736	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11769398	0.86[JPT][hapmap]
rs12668946	0.89[CEU][hapmap];1.00[MEX][hapmap]
rs12673502	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs17545564	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17627961	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17659868	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17710874	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17710880	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2123609	0.89[CEU][hapmap];0.87[AMR][1000 genomes]
rs2348460	0.91[JPT][hapmap]
rs2348462	0.92[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs4724648	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4724650	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6959021	0.89[CEU][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73692834	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9639988	0.88[CEU][hapmap];0.87[AMR][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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv888003	chr7:47694270-47907214	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2290386	URGCP	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47838400-47853600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr7:47846800-47858600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:47847400-47854000	Weak transcription	Fetal Muscle Leg	muscle
4	chr7:47847600-47855800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:47847600-47858800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr7:47847800-47853000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:47847800-47853000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr7:47847800-47854200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:47848000-47853200	Weak transcription	Primary B cells from cord blood	blood
10	chr7:47848200-47853000	Weak transcription	Adipose Nuclei	Adipose
11	chr7:47848400-47853400	Weak transcription	A549	lung
12	chr7:47848400-47857600	Weak transcription	HSMMtube	muscle
13	chr7:47850600-47853000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr7:47851200-47853200	Enhancers	Brain Angular Gyrus	brain
15	chr7:47851200-47853200	Enhancers	Brain Anterior Caudate	brain
16	chr7:47851200-47853400	Enhancers	Brain Substantia Nigra	brain
17	chr7:47851200-47853600	Enhancers	Brain Cingulate Gyrus	brain
18	chr7:47851200-47853600	Enhancers	Brain Hippocampus Middle	brain
19	chr7:47851200-47853600	Enhancers	HepG2	liver
20	chr7:47851200-47853800	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr7:47851200-47854800	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr7:47851200-47855200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr7:47851400-47853200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr7:47851600-47853200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:47852200-47853000	Enhancers	Left Ventricle	heart
26	chr7:47852200-47853000	Enhancers	Lung	lung
27	chr7:47852400-47857800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr7:47852600-47853000	Enhancers	Placenta	Placenta
29	chr7:47852600-47854200	Enhancers	Spleen	Spleen
30	chr7:47852800-47853600	Enhancers	Fetal Intestine Large	intestine
31	chr7:47852800-47853800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr7:47852800-47854000	Enhancers	Fetal Intestine Small	intestine
33	chr7:47852800-47854600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr7:47852800-47855600	Weak transcription	Right Ventricle	heart
35	chr7:47852800-47856000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr7:47852800-47879000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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