Variant report

Variant	rs12871411
Chromosome Location	chr13:49201331-49201332
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1009719	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12050047	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12583212	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12583622	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12585234	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12859099	0.81[EUR][1000 genomes]
rs12864882	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12867110	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12867640	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12870838	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12870872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12871822	0.94[ASN][1000 genomes]
rs12876715	0.94[ASN][1000 genomes]
rs1326697	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359107	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1476406	0.90[ASN][1000 genomes]
rs1980838	0.92[ASN][1000 genomes]
rs1980839	0.92[ASN][1000 genomes]
rs2146861	0.92[ASN][1000 genomes]
rs2148516	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34119347	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs36088391	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59136233	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59927903	0.94[ASN][1000 genomes]
rs7324562	0.85[EUR][1000 genomes]
rs7331325	0.96[ASN][1000 genomes]
rs7987608	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7988330	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7989251	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9535055	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535056	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535058	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9562835	0.84[ASN][1000 genomes]
rs9562836	0.84[ASN][1000 genomes]
rs9568057	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568060	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568063	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568066	0.94[ASN][1000 genomes]
rs9568067	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568068	1.00[ASN][1000 genomes]
rs9568070	0.94[ASN][1000 genomes]
rs9568071	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568072	0.94[ASN][1000 genomes]
rs9568075	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9568077	0.84[ASN][1000 genomes]
rs9634815	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9634816	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9634817	0.96[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	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	nsv832605	chr13:49171305-49344970	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3495983	chr13:49181790-49222165	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3495984	chr13:49181790-49222165	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12871411	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49196600-49201800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr13:49196800-49205600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr13:49197400-49202000	Enhancers	Ovary	ovary
4	chr13:49197600-49202200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr13:49197800-49202000	Enhancers	Placenta	Placenta
6	chr13:49198000-49205000	Enhancers	Fetal Intestine Large	intestine
7	chr13:49199000-49201600	Enhancers	Adipose Nuclei	Adipose
8	chr13:49199000-49202000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr13:49199000-49205000	Enhancers	Fetal Intestine Small	intestine
10	chr13:49199200-49201800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr13:49199400-49201600	Enhancers	Fetal Kidney	kidney
12	chr13:49199400-49201600	Enhancers	NH-A	brain
13	chr13:49199400-49201800	Enhancers	Primary hematopoietic stem cells	blood
14	chr13:49199600-49201400	Weak transcription	Fetal Heart	heart
15	chr13:49199600-49202000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr13:49199600-49202000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr13:49199800-49202000	Enhancers	Stomach Mucosa	stomach
18	chr13:49199800-49204200	Weak transcription	Aorta	Aorta
19	chr13:49200000-49201400	Weak transcription	Right Atrium	heart
20	chr13:49200000-49201600	Enhancers	K562	blood
21	chr13:49200200-49203200	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr13:49200200-49203200	Enhancers	HepG2	liver
23	chr13:49200400-49202000	Flanking Active TSS	Dnd41	blood
24	chr13:49200800-49201600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr13:49200800-49203400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr13:49201000-49202000	Enhancers	Pancreas	Pancrea
27	chr13:49201000-49207400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr13:49201200-49201400	Weak transcription	Gastric	stomach
29	chr13:49201200-49205200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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