Variant report

Variant	rs943280
Chromosome Location	chr13:49169022-49169023
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11148110	0.94[EUR][1000 genomes]
rs12855185	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12859099	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12876717	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12877288	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12877954	0.93[EUR][1000 genomes]
rs1359688	0.84[EUR][1000 genomes]
rs1476406	0.81[ASN][1000 genomes]
rs1536396	0.91[EUR][1000 genomes]
rs1536397	0.93[EUR][1000 genomes]
rs1808060	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1887152	0.86[EUR][1000 genomes]
rs1887154	0.87[EUR][1000 genomes]
rs1894255	0.80[CEU][hapmap]
rs1951775	0.90[CEU][hapmap]
rs198563	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs198584	0.90[CEU][hapmap];0.80[CHB][hapmap];0.84[JPT][hapmap]
rs198590	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs198604	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs198607	0.80[CEU][hapmap];0.80[CHB][hapmap];0.84[JPT][hapmap]
rs198612	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs2104532	0.92[EUR][1000 genomes]
rs2406935	0.85[EUR][1000 genomes]
rs2407093	0.91[EUR][1000 genomes]
rs2407095	0.93[EUR][1000 genomes]
rs2897588	0.83[EUR][1000 genomes]
rs4497565	0.87[EUR][1000 genomes]
rs4635233	0.92[EUR][1000 genomes]
rs7139578	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs7325719	0.82[EUR][1000 genomes]
rs7329065	0.89[EUR][1000 genomes]
rs7332322	0.87[EUR][1000 genomes]
rs7333360	0.87[EUR][1000 genomes]
rs7336379	0.90[EUR][1000 genomes]
rs8002098	0.93[EUR][1000 genomes]
rs9316381	0.90[CEU][hapmap];0.80[CHB][hapmap];0.84[JPT][hapmap]
rs9316388	0.90[CEU][hapmap];0.80[CHB][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs9316393	0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs9316394	0.85[EUR][1000 genomes]
rs9316395	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs9316399	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs9316407	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs943278	0.91[CEU][hapmap]
rs943283	0.83[EUR][1000 genomes]
rs9526479	0.85[EUR][1000 genomes]
rs9526481	0.93[EUR][1000 genomes]
rs9526483	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535032	0.90[CEU][hapmap]
rs9535038	0.91[EUR][1000 genomes]
rs9535042	0.92[EUR][1000 genomes]
rs9535043	0.90[EUR][1000 genomes]
rs9535045	0.92[EUR][1000 genomes]
rs9535046	0.93[EUR][1000 genomes]
rs9535049	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9562819	0.82[CEU][hapmap]
rs9568047	0.85[EUR][1000 genomes]
rs9568049	0.93[EUR][1000 genomes]
rs9568050	0.93[EUR][1000 genomes]
rs9568051	0.82[EUR][1000 genomes]
rs9595937	0.83[EUR][1000 genomes]
rs9634680	0.92[EUR][1000 genomes]
rs990814	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
rs943280	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49161000-49169600	Weak transcription	HSMM	muscle
2	chr13:49161400-49169600	Weak transcription	Right Atrium	heart
3	chr13:49161400-49176400	Weak transcription	Right Ventricle	heart
4	chr13:49163800-49170800	Enhancers	Stomach Mucosa	stomach
5	chr13:49164000-49169800	Enhancers	HepG2	liver
6	chr13:49165000-49169600	Weak transcription	Fetal Muscle Leg	muscle
7	chr13:49165000-49169600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr13:49165200-49169600	Weak transcription	Left Ventricle	heart
9	chr13:49165200-49169600	Weak transcription	Small Intestine	intestine
10	chr13:49165400-49169600	Weak transcription	Gastric	stomach
11	chr13:49165400-49169600	Weak transcription	Pancreas	Pancrea
12	chr13:49165400-49169600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr13:49165400-49169600	Weak transcription	HSMMtube	muscle
14	chr13:49165600-49169600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr13:49165800-49170000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr13:49166000-49170000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr13:49166000-49170000	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr13:49166200-49173800	Weak transcription	Fetal Kidney	kidney
19	chr13:49166400-49170000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr13:49166600-49169200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr13:49166600-49169600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr13:49166600-49169600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr13:49166800-49169800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr13:49167000-49169800	Enhancers	Duodenum Mucosa	Duodenum
25	chr13:49167400-49169800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr13:49167400-49169800	Enhancers	H9 Cell Line	embryonic stem cell
27	chr13:49167400-49170200	Enhancers	GM12878-XiMat	blood
28	chr13:49167400-49170400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr13:49167400-49170400	Enhancers	Placenta	Placenta
30	chr13:49167800-49169800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr13:49168000-49169200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr13:49168000-49169600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr13:49168200-49169600	Weak transcription	NH-A	brain
34	chr13:49168200-49174800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr13:49168400-49175000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr13:49168600-49169400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr13:49168600-49170000	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr13:49168600-49170000	Weak transcription	Adipose Nuclei	Adipose
39	chr13:49168600-49170400	Enhancers	Fetal Intestine Small	intestine
40	chr13:49168800-49169600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr13:49168800-49170400	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr13:49169000-49169400	Weak transcription	Hela-S3	cervix
43	chr13:49169000-49169600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr13:49169000-49170200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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