Variant report

Variant	rs2897588
Chromosome Location	chr13:49088454-49088455
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49081743..49084542-chr13:49085954..49089235,3	K562	blood:
2	chr13:49088221..49089957-chr13:49104157..49106836,2	MCF-7	breast:
3	chr13:49087919..49090569-chr13:49105572..49108437,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136161	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12877954	0.80[EUR][1000 genomes]
rs1359688	0.84[EUR][1000 genomes]
rs1536397	0.80[EUR][1000 genomes]
rs1951775	0.85[EUR][1000 genomes]
rs198584	0.81[EUR][1000 genomes]
rs198590	0.81[EUR][1000 genomes]
rs2104532	0.81[EUR][1000 genomes]
rs2406935	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407093	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2407095	0.81[EUR][1000 genomes]
rs3092904	0.81[EUR][1000 genomes]
rs4635233	0.81[EUR][1000 genomes]
rs7139578	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7329065	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7333360	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7336379	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8002098	0.81[EUR][1000 genomes]
rs9316381	0.81[EUR][1000 genomes]
rs9316382	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9316388	0.86[EUR][1000 genomes]
rs9316393	0.86[EUR][1000 genomes]
rs9316394	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316395	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9316399	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs943278	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs943280	0.83[EUR][1000 genomes]
rs943283	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526479	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526481	0.80[EUR][1000 genomes]
rs9535032	0.86[EUR][1000 genomes]
rs9535033	0.85[EUR][1000 genomes]
rs9535035	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535038	0.81[EUR][1000 genomes]
rs9535045	0.81[EUR][1000 genomes]
rs9535046	0.80[EUR][1000 genomes]
rs9568043	0.92[EUR][1000 genomes]
rs9568047	0.83[EUR][1000 genomes]
rs9568049	0.80[EUR][1000 genomes]
rs9568050	0.80[EUR][1000 genomes]
rs9634680	0.81[EUR][1000 genomes]
rs990814	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv983709	chr13:49086347-49097905	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2897588	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49054000-49094000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:49067200-49105200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr13:49067200-49105400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr13:49067800-49098000	Weak transcription	Right Ventricle	heart
5	chr13:49068000-49105600	Weak transcription	Gastric	stomach
6	chr13:49068200-49102600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr13:49071200-49105600	Weak transcription	Fetal Brain Male	brain
8	chr13:49071800-49105800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr13:49072200-49095600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:49075600-49093400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr13:49075600-49095200	Weak transcription	Fetal Intestine Large	intestine
12	chr13:49075800-49093200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr13:49076600-49097400	Weak transcription	Pancreas	Pancrea
14	chr13:49079600-49091000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr13:49079600-49092200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr13:49080600-49105600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr13:49080800-49102200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr13:49080800-49105400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr13:49081000-49090200	Weak transcription	HSMM	muscle
20	chr13:49081400-49088600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr13:49081400-49105600	Weak transcription	Placenta	Placenta
22	chr13:49083400-49094400	Weak transcription	Fetal Intestine Small	intestine
23	chr13:49083400-49095800	Weak transcription	Spleen	Spleen
24	chr13:49083800-49105600	Weak transcription	Esophagus	oesophagus
25	chr13:49085000-49091200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr13:49085000-49096000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr13:49085000-49096600	Weak transcription	Small Intestine	intestine
28	chr13:49085000-49104800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr13:49085000-49104800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr13:49085200-49096000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr13:49085200-49100400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr13:49085200-49105600	Weak transcription	Fetal Thymus	thymus
33	chr13:49085600-49089600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr13:49086200-49088800	Weak transcription	Liver	Liver
35	chr13:49086200-49089200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr13:49086200-49090000	Weak transcription	Brain Hippocampus Middle	brain
37	chr13:49086200-49090400	Weak transcription	Fetal Stomach	stomach
38	chr13:49086200-49090800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr13:49086200-49091200	Weak transcription	Psoas Muscle	Psoas
40	chr13:49086200-49091200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr13:49086200-49094400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr13:49086200-49102200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr13:49086200-49102400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr13:49086200-49105600	Weak transcription	Lung	lung
45	chr13:49086200-49105600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr13:49086200-49105600	Weak transcription	HSMMtube	muscle
47	chr13:49086400-49089400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr13:49086400-49089600	Weak transcription	Brain Substantia Nigra	brain
49	chr13:49086400-49089800	Weak transcription	Brain Anterior Caudate	brain
50	chr13:49086400-49090200	Weak transcription	Right Atrium	heart

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