Variant report

Variant	rs7358800
Chromosome Location	chr13:111012857-111012858
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10161783	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10161785	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10220229	1.00[CEU][hapmap]
rs2094701	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4771671	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4771672	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9521713	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9555690	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9555691	0.85[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9559775	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7358800	RCN3	trans	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:110994000-111019600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr13:111000600-111013800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr13:111000800-111019800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr13:111002000-111015200	Weak transcription	Brain Substantia Nigra	brain
5	chr13:111002400-111026000	Weak transcription	Psoas Muscle	Psoas
6	chr13:111006000-111013000	Weak transcription	Spleen	Spleen
7	chr13:111007400-111023000	Weak transcription	A549	lung
8	chr13:111007600-111013200	Weak transcription	Fetal Lung	lung
9	chr13:111007600-111013200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr13:111007600-111020400	Weak transcription	Fetal Kidney	kidney
11	chr13:111007600-111030600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr13:111007600-111031000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr13:111007600-111031400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr13:111007800-111013000	Weak transcription	Colonic Mucosa	Colon
15	chr13:111007800-111013600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr13:111007800-111018000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr13:111008400-111020000	Weak transcription	HMEC	breast
18	chr13:111008600-111018000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr13:111008800-111013200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr13:111008800-111015400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr13:111009000-111013200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr13:111009000-111014200	Weak transcription	Esophagus	oesophagus
23	chr13:111009000-111018000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr13:111009000-111024000	Weak transcription	Pancreas	Pancrea
25	chr13:111009000-111029400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr13:111009600-111013000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr13:111009800-111016200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr13:111009800-111018400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr13:111010200-111016000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr13:111010400-111013000	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr13:111010400-111024000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr13:111011000-111013000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr13:111011000-111013200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr13:111011000-111014000	Weak transcription	Fetal Intestine Small	intestine
35	chr13:111011000-111016400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr13:111011000-111016800	Weak transcription	Fetal Intestine Large	intestine
37	chr13:111011000-111022000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr13:111011000-111024000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr13:111011000-111032000	Weak transcription	Gastric	stomach
40	chr13:111011000-111032400	Weak transcription	NHEK	skin
41	chr13:111011200-111015400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr13:111011200-111016800	Enhancers	Colon Smooth Muscle	Colon
43	chr13:111011200-111029800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr13:111011400-111013200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr13:111011400-111013800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr13:111011400-111016600	Enhancers	Rectal Smooth Muscle	rectum
47	chr13:111011600-111013000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr13:111011600-111014600	Genic enhancers	NH-A	brain
49	chr13:111011600-111015400	Enhancers	NHDF-Ad	bronchial
50	chr13:111011600-111015600	Genic enhancers	Fetal Stomach	stomach

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