Variant report

Variant	rs6562923
Chromosome Location	chr13:76449465-76449466
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1015694	0.83[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1036867	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1036868	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10507835	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1323565	1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1323566	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1323567	1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1399	1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1400	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1550620	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2120066	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs4329801	0.96[ASN][1000 genomes]
rs4418941	0.95[ASN][1000 genomes]
rs4508318	0.96[ASN][1000 genomes]
rs4572275	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4598784	0.96[ASN][1000 genomes]
rs4884024	0.83[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4885358	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4885359	0.95[ASN][1000 genomes]
rs4885360	0.95[ASN][1000 genomes]
rs4885361	0.95[ASN][1000 genomes]
rs4885362	0.81[ASN][1000 genomes]
rs7981821	0.83[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7986419	0.83[ASN][1000 genomes]
rs7986876	1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7987971	0.96[ASN][1000 genomes]
rs7995080	0.95[ASN][1000 genomes]
rs9318381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9530477	1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9530479	0.93[ASN][1000 genomes]
rs9530481	0.95[ASN][1000 genomes]
rs9530483	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9530484	0.81[ASN][1000 genomes]
rs9544060	0.83[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs9544061	0.84[GIH][hapmap]
rs9544069	0.95[ASN][1000 genomes]
rs9544071	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9593137	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9600572	0.83[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs9600574	0.83[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs9600575	0.83[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs9600577	0.83[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs9600578	1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9600579	1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9600581	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9600582	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs969394	0.83[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]

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	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv832649	chr13:76424872-76657891	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6562923	LMO7	cis	parietal	SCAN
rs6562923	C13orf45	cis	Nerve Tibial	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76440000-76469200	Weak transcription	HSMM	muscle
2	chr13:76444400-76451000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr13:76444600-76449600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr13:76444800-76450400	Weak transcription	Fetal Heart	heart
5	chr13:76445000-76449600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr13:76445000-76450200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr13:76445000-76450200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:76445000-76450400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr13:76445000-76450400	Weak transcription	Fetal Intestine Small	intestine
10	chr13:76445000-76450400	Weak transcription	GM12878-XiMat	blood
11	chr13:76445000-76450600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr13:76445000-76450800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr13:76445000-76451000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr13:76445200-76449800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr13:76445200-76450000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr13:76445200-76450200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr13:76445200-76450400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr13:76445200-76451000	Weak transcription	Colon Smooth Muscle	Colon
19	chr13:76445400-76449800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr13:76445400-76450400	Weak transcription	A549	lung
21	chr13:76445400-76454400	Weak transcription	Osteobl	bone
22	chr13:76445600-76450400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr13:76445600-76450400	Weak transcription	Fetal Brain Female	brain
24	chr13:76445600-76453400	Weak transcription	Adipose Nuclei	Adipose
25	chr13:76445600-76453600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr13:76446000-76449800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr13:76446000-76450400	Weak transcription	Fetal Muscle Leg	muscle
28	chr13:76447400-76449600	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr13:76447800-76449600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr13:76448400-76450400	Weak transcription	HMEC	breast
31	chr13:76449000-76449800	Enhancers	H1 Cell Line	embryonic stem cell
32	chr13:76449000-76451000	Enhancers	Primary T cells from cord blood	blood
33	chr13:76449000-76451200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr13:76449000-76451600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr13:76449200-76450400	Weak transcription	Fetal Lung	lung
36	chr13:76449200-76451000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr13:76449400-76449600	Enhancers	Fetal Brain Male	brain
38	chr13:76449400-76449600	Enhancers	Fetal Thymus	thymus
39	chr13:76449400-76449800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr13:76449400-76450400	Enhancers	Monocytes-CD14+_RO01746	blood

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