Variant report

Variant	rs12877954
Chromosome Location	chr13:49167365-49167366
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11148110	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12855185	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12859099	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12876717	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12877288	0.92[EUR][1000 genomes]
rs1359688	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1536396	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536397	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808060	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1887154	0.81[EUR][1000 genomes]
rs198584	0.84[EUR][1000 genomes]
rs198590	0.85[EUR][1000 genomes]
rs2104532	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2406935	0.83[EUR][1000 genomes]
rs2407093	0.88[EUR][1000 genomes]
rs2407095	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2897588	0.80[EUR][1000 genomes]
rs3092904	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4497565	0.81[EUR][1000 genomes]
rs4635233	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7139578	0.85[EUR][1000 genomes]
rs7325719	0.83[EUR][1000 genomes]
rs7329065	0.86[EUR][1000 genomes]
rs7332322	0.80[EUR][1000 genomes]
rs7333360	0.84[EUR][1000 genomes]
rs7336379	0.87[EUR][1000 genomes]
rs8002098	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316381	0.85[EUR][1000 genomes]
rs9316388	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9316393	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9316394	0.83[EUR][1000 genomes]
rs9316395	0.83[EUR][1000 genomes]
rs9316399	0.83[EUR][1000 genomes]
rs9316407	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs943280	0.93[EUR][1000 genomes]
rs943283	0.80[EUR][1000 genomes]
rs9526479	0.83[EUR][1000 genomes]
rs9526481	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526483	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535038	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535042	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535043	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535045	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535046	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535049	0.92[EUR][1000 genomes]
rs9568047	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568049	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568050	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568051	0.83[EUR][1000 genomes]
rs9634680	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv455881	chr13:49134412-49169570	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv561591	chr13:49134412-49169570	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12877954	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49161000-49169600	Weak transcription	HSMM	muscle
2	chr13:49161200-49167400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:49161200-49167400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr13:49161400-49169600	Weak transcription	Right Atrium	heart
5	chr13:49161400-49176400	Weak transcription	Right Ventricle	heart
6	chr13:49163600-49167400	Enhancers	Fetal Intestine Large	intestine
7	chr13:49163800-49168200	Enhancers	Fetal Intestine Small	intestine
8	chr13:49163800-49170800	Enhancers	Stomach Mucosa	stomach
9	chr13:49164000-49169800	Enhancers	HepG2	liver
10	chr13:49165000-49169600	Weak transcription	Fetal Muscle Leg	muscle
11	chr13:49165000-49169600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr13:49165200-49169600	Weak transcription	Left Ventricle	heart
13	chr13:49165200-49169600	Weak transcription	Small Intestine	intestine
14	chr13:49165400-49167400	Weak transcription	Placenta	Placenta
15	chr13:49165400-49167800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr13:49165400-49168000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr13:49165400-49169600	Weak transcription	Gastric	stomach
18	chr13:49165400-49169600	Weak transcription	Pancreas	Pancrea
19	chr13:49165400-49169600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr13:49165400-49169600	Weak transcription	HSMMtube	muscle
21	chr13:49165600-49168400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr13:49165600-49168800	Weak transcription	Hela-S3	cervix
23	chr13:49165600-49169600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr13:49165800-49170000	Enhancers	H1 Cell Line	embryonic stem cell
25	chr13:49166000-49168200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr13:49166000-49170000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr13:49166000-49170000	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr13:49166200-49167400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr13:49166200-49173800	Weak transcription	Fetal Kidney	kidney
30	chr13:49166400-49170000	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr13:49166600-49167400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr13:49166600-49167600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr13:49166600-49167600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr13:49166600-49168400	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr13:49166600-49169200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr13:49166600-49169600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr13:49166600-49169600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr13:49166800-49169000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr13:49166800-49169800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr13:49167000-49167400	Weak transcription	GM12878-XiMat	blood
41	chr13:49167000-49167600	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr13:49167000-49167800	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr13:49167000-49168600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr13:49167000-49169800	Enhancers	Duodenum Mucosa	Duodenum
45	chr13:49167200-49168000	Enhancers	Primary monocytes fromperipheralblood	blood

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