Variant report

Variant	rs12100135
Chromosome Location	chr13:48807004-48807005
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	UBTF	chr13:48806958-48808141	K562	blood:	n/a	n/a
2	POLR2A	chr13:48806994-48808013	K562	blood:	n/a	n/a
3	E2F6	chr13:48806990-48807892	K562	blood:	n/a	chr13:48807460-48807470 chr13:48807852-48807861 chr13:48807701-48807710 chr13:48807459-48807468
4	RAD21	chr13:48806892-48807223	HepG2	liver:	n/a	n/a
5	POLR2A	chr13:48806843-48808079	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr13:48806925-48807220	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr13:48806854-48808083	NB4	blood:	n/a	n/a
8	TBP	chr13:48806857-48808013	HepG2	liver:	n/a	n/a
9	TAF1	chr13:48806769-48808127	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr13:48806958-48807627	HCT-116	colon:	n/a	n/a
11	MXI1	chr13:48806484-48808649	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr13:48806897-48807200	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr13:48806942-48808012	MCF-7	breast:	n/a	n/a
14	REST	chr13:48806764-48807510	HepG2	liver:	n/a	chr13:48807168-48807181 chr13:48807200-48807213 chr13:48807308-48807318
15	E2F4	chr13:48806862-48807463	MCF10A-Er-Src	breast:	n/a	n/a
16	MXI1	chr13:48806509-48808033	HepG2	liver:	n/a	n/a
17	MAX	chr13:48806515-48808286	NB4	blood:	n/a	n/a
18	POLR2A	chr13:48806952-48807226	HepG2	liver:	n/a	n/a
19	MAZ	chr13:48806850-48807824	GM12878	blood:	n/a	n/a
20	POLR2A	chr13:48806963-48807700	HEK293	kidney:	n/a	n/a
21	HEY1	chr13:48806978-48807226	K562	blood:	n/a	n/a
22	REST	chr13:48806916-48808562	H1-neurons	neurons:	n/a	chr13:48807665-48807678 chr13:48807168-48807181 chr13:48807772-48807780 chr13:48807642-48807655 chr13:48807888-48807901 chr13:48807200-48807213 chr13:48807308-48807318
23	YY1	chr13:48806914-48808074	HepG2	liver:	n/a	chr13:48807446-48807460 chr13:48807664-48807678 chr13:48807459-48807468 chr13:48807479-48807493 chr13:48807454-48807468 chr13:48807462-48807471 chr13:48808006-48808018
24	POLR2A	chr13:48806291-48808234	HepG2	liver:	n/a	n/a
25	RAD21	chr13:48806776-48808109	H1-hESC	embryonic stem cell:	n/a	chr13:48807688-48807702 chr13:48807940-48807954
26	MAZ	chr13:48806614-48807974	K562	blood:	n/a	n/a
27	POLR2A	chr13:48806883-48808018	MCF-7	breast:	n/a	n/a
28	HEY1	chr13:48806939-48807525	HepG2	liver:	n/a	n/a
29	POLR2A	chr13:48806967-48808014	K562	blood:	n/a	n/a
30	POLR2A	chr13:48806863-48807958	ProgFib	skin:	n/a	n/a
31	TEAD4	chr13:48806679-48807128	HepG2	liver:	n/a	n/a
32	NFIC	chr13:48806669-48807250	HepG2	liver:	n/a	n/a
33	TEAD4	chr13:48806801-48807407	ECC-1	luminal epithelium:	n/a	n/a
34	TAF1	chr13:48806927-48808181	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr13:48806973-48808013	K562	blood:	n/a	n/a
36	TBP	chr13:48806769-48808304	H1-hESC	embryonic stem cell:	n/a	n/a
37	RCOR1	chr13:48806486-48807904	HepG2	liver:	n/a	n/a
38	TAF1	chr13:48806936-48808108	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr13:48806991-48807217	HepG2	liver:	n/a	n/a
40	HDAC2	chr13:48806925-48807401	HepG2	liver:	n/a	n/a
41	POLR2A	chr13:48806947-48808237	K562	blood:	n/a	n/a
42	SIN3A	chr13:48806774-48808396	H1-hESC	embryonic stem cell:	n/a	chr13:48807639-48807648 chr13:48807193-48807204 chr13:48807642-48807655 chr13:48807680-48807691
43	POLR2A	chr13:48806973-48808236	K562	blood:	n/a	n/a
44	MBD4	chr13:48806581-48807220	HepG2	liver:	n/a	n/a
45	POLR2A	chr13:48806879-48809159	MCF10A-Er-Src	breast:	n/a	n/a
46	SMC3	chr13:48806820-48807171	HepG2	liver:	n/a	n/a
47	TEAD4	chr13:48806862-48807335	ECC-1	luminal epithelium:	n/a	n/a
48	MAX	chr13:48806906-48807523	A549	lung:	n/a	n/a
49	TAF1	chr13:48806987-48807842	HepG2	liver:	n/a	n/a
50	RCOR1	chr13:48806950-48807184	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:48806118..48810225-chr13:48876144..48879386,12	MCF-7	breast:
2	chr13:48806307..48808548-chr13:49152200..49154470,2	MCF-7	breast:
3	chr13:48612019..48613651-chr13:48806032..48808331,2	MCF-7	breast:
4	chr13:48806544..48809798-chr13:48876519..48878974,4	K562	blood:
5	chr13:48805537..48807049-chr13:48830310..48832562,2	K562	blood:
6	chr13:48806826..48807726-chr6:111804447..111805411,2	HCT-116	colon:
7	chr13:48806625..48809806-chr13:48877426..48879405,3	K562	blood:
8	chr13:48667865..48670263-chr13:48806295..48809101,2	MCF-7	breast:
9	chr13:48668651..48670754-chr13:48805441..48808765,3	MCF-7	breast:

Variant related genes	Relation type
ITM2B	TF binding region
ENSG00000139687	Chromatin interaction
ENSG00000231889	Chromatin interaction
ENSG00000231473	Chromatin interaction
ENSG00000233610	Chromatin interaction
ENSG00000136146	Chromatin interaction
ENSG00000136143	Chromatin interaction
ENSG00000009413	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10219833	0.89[EUR][1000 genomes]
rs12430215	0.85[CEU][hapmap]
rs12871662	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12871740	0.94[EUR][1000 genomes]
rs12875750	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1573601	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1886795	0.91[EUR][1000 genomes]
rs1894255	0.80[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap]
rs1925744	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1925745	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1981434	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs198604	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs198607	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs198612	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs198619	0.95[CEU][hapmap]
rs198634	0.84[ASN][1000 genomes]
rs2243461	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2243626	0.90[CEU][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs2248488	0.85[CEU][hapmap];0.95[EUR][1000 genomes]
rs2251813	0.93[EUR][1000 genomes]
rs2253520	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2254423	0.93[EUR][1000 genomes]
rs2406933	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2854345	0.83[ASN][1000 genomes]
rs34217484	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3803188	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3809328	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3818455	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs399413	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs4151450	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs4594153	0.91[EUR][1000 genomes]
rs4600372	0.88[EUR][1000 genomes]
rs520342	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs61973349	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7322987	0.86[EUR][1000 genomes]
rs7337883	0.80[EUR][1000 genomes]
rs7358982	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7984554	0.94[EUR][1000 genomes]
rs7984795	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs7999447	0.89[EUR][1000 genomes]
rs8001315	0.94[EUR][1000 genomes]
rs9316367	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9316369	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526465	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs9526466	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9526470	0.84[EUR][1000 genomes]
rs9526475	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs9534996	0.87[EUR][1000 genomes]
rs9534998	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535000	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535002	0.93[EUR][1000 genomes]
rs9535003	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535006	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535007	0.91[EUR][1000 genomes]
rs9535009	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535011	0.89[EUR][1000 genomes]
rs9562819	0.80[CEU][hapmap]
rs9568025	0.86[ASN][1000 genomes]
rs9568026	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9568027	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9568028	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9568029	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs9568032	0.84[ASN][1000 genomes]
rs9568033	0.84[ASN][1000 genomes]
rs9568034	0.84[ASN][1000 genomes]
rs9568035	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1043294	chr13:48762477-48810028	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12100135	ITM2B	cis	lymphoblastoid	seeQTL
rs12100135	LPAR6	cis	parietal	SCAN
rs12100135	DLEU1	cis	parietal	SCAN
rs12100135	ATAD2	trans	parietal	SCAN
rs12100135	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48806000-48808200	Active TSS	Primary hematopoietic stem cells	blood
2	chr13:48806200-48809800	Active TSS	Brain Angular Gyrus	brain
3	chr13:48806400-48807200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr13:48806400-48807200	Flanking Active TSS	Dnd41	blood
5	chr13:48806400-48807400	Active TSS	Fetal Brain Female	brain
6	chr13:48806600-48807200	Flanking Active TSS	Liver	Liver
7	chr13:48806600-48807400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr13:48806600-48807400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr13:48806600-48807400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr13:48806600-48807400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr13:48806600-48808400	Active TSS	H9 Cell Line	embryonic stem cell
12	chr13:48806600-48808400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr13:48806600-48808600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr13:48806600-48808800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:48806600-48809200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr13:48806600-48809400	Active TSS	HSMM	muscle
17	chr13:48806600-48809800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr13:48806600-48809800	Active TSS	H1 Cell Line	embryonic stem cell
19	chr13:48806600-48809800	Active TSS	Brain Substantia Nigra	brain
20	chr13:48806600-48810000	Active TSS	Colonic Mucosa	Colon
21	chr13:48806600-48810000	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr13:48806600-48810000	Active TSS	NHLF	lung
23	chr13:48806600-48810400	Active TSS	Aorta	Aorta
24	chr13:48806600-48811000	Active TSS	Psoas Muscle	Psoas
25	chr13:48806600-48811000	Active TSS	Right Ventricle	heart
26	chr13:48806600-48812200	Active TSS	Ovary	ovary
27	chr13:48806600-48812200	Active TSS	Right Atrium	heart
28	chr13:48806800-48807200	Flanking Active TSS	GM12878-XiMat	blood
29	chr13:48806800-48807200	Flanking Active TSS	HSMMtube	muscle
30	chr13:48806800-48807800	Active TSS	HepG2	liver
31	chr13:48806800-48808200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr13:48806800-48808200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
33	chr13:48806800-48808400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr13:48806800-48808400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr13:48806800-48808400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr13:48806800-48808400	Active TSS	Esophagus	oesophagus
37	chr13:48806800-48808400	Active TSS	Gastric	stomach
38	chr13:48806800-48808400	Active TSS	Pancreas	Pancrea
39	chr13:48806800-48808400	Active TSS	Placenta Amnion	Placenta Amnion
40	chr13:48806800-48808400	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr13:48806800-48808400	Active TSS	Small Intestine	intestine
42	chr13:48806800-48808600	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr13:48806800-48808600	Active TSS	Stomach Mucosa	stomach
44	chr13:48806800-48808800	Active TSS	Fetal Heart	heart
45	chr13:48806800-48809200	Active TSS	NH-A	brain
46	chr13:48806800-48809400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr13:48806800-48809400	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr13:48806800-48809400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr13:48806800-48809400	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr13:48806800-48809400	Active TSS	Primary T killer naive cells fromperipheralblood	blood

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