Variant report

Variant	rs13004700
Chromosome Location	chr2:99527568-99527569
allele	C/T
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	MYBL2	chr2:99527375-99528050	HepG2	liver:	n/a	n/a
2	FOXA1	chr2:99527555-99528057	HepG2	liver:	n/a	n/a
3	MAX	chr2:99527493-99528206	HepG2	liver:	n/a	chr2:99527880-99527889 chr2:99527575-99527584

No.	Distal block	Cell Line	Cell type
1	chr2:99514144..99517054-chr2:99525112..99527785,2	MCF-7	breast:
2	chr2:99484412..99487919-chr2:99523957..99528531,6	MCF-7	breast:
3	chr2:99525536..99528520-chr2:99541090..99543085,2	MCF-7	breast:

Variant related genes	Relation type
KIAA1211L	TF binding region
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10169003	0.82[EUR][1000 genomes]
rs10172158	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10181972	0.82[EUR][1000 genomes]
rs10192266	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11123755	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11893888	0.82[EUR][1000 genomes]
rs12468024	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12474283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712038	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12712041	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712042	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12712043	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13004923	0.82[EUR][1000 genomes]
rs13005124	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13011428	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025076	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13025913	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13028500	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1581250	0.82[EUR][1000 genomes]
rs1581251	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1607256	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17758170	0.88[CEU][hapmap]
rs1878585	0.82[EUR][1000 genomes]
rs1878589	0.85[CEU][hapmap]
rs1976766	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4311103	0.96[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4850889	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4850890	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4851167	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4851170	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851171	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851173	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851174	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs4851175	0.88[CEU][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4851176	0.83[AFR][1000 genomes]
rs4851177	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56125264	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6419564	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542841	0.81[CEU][hapmap]
rs6542843	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542845	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6714243	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6717372	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6724477	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs6739176	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6739503	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6742047	0.84[AMR][1000 genomes]
rs6757098	0.84[CEU][hapmap]
rs6760065	0.84[CEU][hapmap]
rs7423519	0.88[CEU][hapmap]
rs7608889	0.85[CEU][hapmap];0.87[CHB][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs883773	0.81[CEU][hapmap]
rs908672	0.82[AFR][1000 genomes]
rs925887	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582518	chr2:99498774-99546355	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv874697	chr2:99520608-99558970	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13004700	TSGA10	cis	Lymphoblastoid	GTEx
rs13004700	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99520800-99528600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:99523800-99530000	Enhancers	Fetal Muscle Leg	muscle
3	chr2:99524400-99528400	Enhancers	HMEC	breast
4	chr2:99524400-99534400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:99524600-99532400	Enhancers	Pancreas	Pancrea
6	chr2:99525200-99530600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr2:99525800-99529600	Weak transcription	Brain Angular Gyrus	brain
8	chr2:99526000-99528000	Enhancers	Gastric	stomach
9	chr2:99526000-99530400	Enhancers	Brain Anterior Caudate	brain
10	chr2:99526000-99530800	Enhancers	Spleen	Spleen
11	chr2:99526200-99527800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr2:99526400-99528000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:99526400-99528000	Weak transcription	NHDF-Ad	bronchial
14	chr2:99526400-99528200	Weak transcription	A549	lung
15	chr2:99526400-99528200	Weak transcription	NHLF	lung
16	chr2:99526400-99528400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:99526400-99528600	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:99526400-99528800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:99526400-99528800	Weak transcription	Right Ventricle	heart
20	chr2:99526400-99529000	Enhancers	Fetal Intestine Large	intestine
21	chr2:99526400-99530200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:99526400-99534200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:99526600-99527600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:99526600-99527600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:99526600-99527600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:99526600-99527600	Weak transcription	Fetal Intestine Small	intestine
27	chr2:99526600-99527600	Weak transcription	NH-A	brain
28	chr2:99526600-99528000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:99526600-99528000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr2:99526600-99528000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:99526600-99528000	Weak transcription	HSMMtube	muscle
32	chr2:99526600-99528200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:99526600-99528200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:99526600-99528400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:99526600-99528400	Weak transcription	Fetal Brain Male	brain
36	chr2:99526600-99528400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:99526600-99528400	Weak transcription	Stomach Mucosa	stomach
38	chr2:99526600-99528600	Weak transcription	Brain Germinal Matrix	brain
39	chr2:99526600-99528600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr2:99526600-99528600	Weak transcription	Fetal Brain Female	brain
41	chr2:99526600-99528800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:99526600-99528800	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr2:99526600-99528800	Weak transcription	Fetal Heart	heart
44	chr2:99526600-99528800	Weak transcription	Lung	lung
45	chr2:99526600-99528800	Weak transcription	Ovary	ovary
46	chr2:99526600-99529000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:99526600-99529800	Enhancers	HUVEC	blood vessel
48	chr2:99526600-99530400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr2:99526600-99530400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:99526600-99533400	Weak transcription	Left Ventricle	heart

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