Variant report

Variant	rs943278
Chromosome Location	chr13:49070174-49070175
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49068490..49070652-chr13:49071490..49073250,2	K562	blood:
2	chr13:49070136..49072576-chr13:49104860..49107906,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136161	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11839271	0.85[AFR][1000 genomes]
rs12430215	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs1573601	0.86[CEU][hapmap]
rs1894255	0.81[CEU][hapmap]
rs1951775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1981434	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs198563	0.91[CEU][hapmap]
rs198584	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs198590	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs198607	0.81[CEU][hapmap]
rs198612	0.86[CEU][hapmap]
rs198619	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2227311	0.82[YRI][hapmap]
rs2406935	0.89[EUR][1000 genomes]
rs2407093	0.84[EUR][1000 genomes]
rs2897588	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3092877	1.00[YRI][hapmap]
rs3092904	0.85[EUR][1000 genomes]
rs399413	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4151450	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4151510	1.00[YRI][hapmap]
rs520342	0.86[CEU][hapmap]
rs7139578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs7329065	0.86[EUR][1000 genomes]
rs7333360	0.88[EUR][1000 genomes]
rs7336379	0.83[EUR][1000 genomes]
rs9316381	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs9316382	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316388	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs9316393	0.80[EUR][1000 genomes]
rs9316394	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9316395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9316399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs943283	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9526475	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9526479	0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs9535032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535033	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535035	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9562819	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9568042	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9568043	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs990814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs943278	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49023800-49073800	Weak transcription	NH-A	brain
2	chr13:49028000-49071000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr13:49030600-49070600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr13:49034400-49073800	Weak transcription	Esophagus	oesophagus
5	chr13:49035200-49073400	Weak transcription	Fetal Intestine Small	intestine
6	chr13:49053600-49071200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr13:49054000-49094000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:49061400-49072000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr13:49062600-49070800	Weak transcription	Fetal Brain Male	brain
10	chr13:49062800-49070400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr13:49062800-49072000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr13:49063000-49087800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr13:49063200-49071000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr13:49064200-49075200	Weak transcription	Fetal Intestine Large	intestine
15	chr13:49064600-49070600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr13:49064800-49071200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr13:49065000-49070200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr13:49065400-49072000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr13:49066800-49073200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr13:49066800-49080200	Weak transcription	Colonic Mucosa	Colon
21	chr13:49067000-49070200	Weak transcription	Aorta	Aorta
22	chr13:49067000-49071400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr13:49067000-49071600	Weak transcription	HepG2	liver
24	chr13:49067000-49072800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr13:49067000-49074600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr13:49067000-49080200	Weak transcription	Psoas Muscle	Psoas
27	chr13:49067000-49084200	Weak transcription	Ovary	ovary
28	chr13:49067200-49071400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr13:49067200-49071800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr13:49067200-49072400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr13:49067200-49072400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr13:49067200-49073200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr13:49067200-49074600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr13:49067200-49079200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr13:49067200-49079600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr13:49067200-49080200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr13:49067200-49105200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr13:49067200-49105400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr13:49067400-49072000	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr13:49067600-49070400	Weak transcription	Thymus	Thymus
41	chr13:49067600-49071600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:49067800-49071000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr13:49067800-49071400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr13:49067800-49072000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr13:49067800-49072000	Weak transcription	Spleen	Spleen
46	chr13:49067800-49073200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr13:49067800-49074800	Weak transcription	Left Ventricle	heart
48	chr13:49067800-49074800	Weak transcription	NHLF	lung
49	chr13:49067800-49078600	Weak transcription	Placenta	Placenta
50	chr13:49067800-49078600	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links