Variant report

Variant	rs7254192
Chromosome Location	chr19:41273699-41273700
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	POLR2A	chr19:41273542-41273799	MCF-7	breast:	n/a	n/a
2	POLR2A	chr19:41273512-41273830	K562	blood:	n/a	n/a
3	POLR2A	chr19:41271325-41274974	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:41271310-41274003	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr19:41273180-41273886	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41256102..41258357-chr19:41273120..41276107,2	MCF-7	breast:
2	chr19:41270648..41272782-chr19:41273219..41274815,2	MCF-7	breast:
3	chr19:41271869..41274092-chr19:41280828..41283092,2	MCF-7	breast:

Variant related genes	Relation type
MIA-RAB4B	TF binding region
MIA	TF binding region
ENSG00000261857	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000077312	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12151282	0.92[ASN][1000 genomes]
rs12973666	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17726276	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279011	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305797	0.98[ASN][1000 genomes]
rs35858034	0.86[ASN][1000 genomes]
rs7245595	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1802033	chr19:41256131-41284240	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	40 gene(s)	inside rSNPs	diseases
2	esv1801805	chr19:41256581-41284363	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	37 gene(s)	inside rSNPs	diseases
3	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7254192	RAB4B,MIA	cis	brain	BrainEAC
rs7254192	C19orf54	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41258000-41283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41259000-41275200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:41260600-41277200	Strong transcription	Fetal Brain Female	brain
4	chr19:41260800-41283200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:41261600-41275000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:41261600-41275200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr19:41261800-41276800	Strong transcription	Fetal Intestine Small	intestine
8	chr19:41261800-41278200	Strong transcription	Fetal Stomach	stomach
9	chr19:41261800-41282800	Weak transcription	Right Atrium	heart
10	chr19:41262000-41276200	Strong transcription	Thymus	Thymus
11	chr19:41262200-41273800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:41262800-41275200	Strong transcription	Liver	Liver
13	chr19:41263000-41273800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr19:41263000-41273800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:41263000-41273800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr19:41263000-41274000	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr19:41263400-41273800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr19:41263400-41274000	Strong transcription	Colonic Mucosa	Colon
19	chr19:41263400-41275200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr19:41264600-41278000	Strong transcription	A549	lung
21	chr19:41270000-41273800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:41270400-41282600	Weak transcription	Fetal Brain Male	brain
23	chr19:41271800-41275200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr19:41271800-41276800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr19:41271800-41279800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:41271800-41279800	Weak transcription	HMEC	breast
27	chr19:41271800-41282600	Weak transcription	Fetal Kidney	kidney
28	chr19:41271800-41282600	Weak transcription	HSMM	muscle
29	chr19:41271800-41283000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr19:41272000-41274400	Weak transcription	GM12878-XiMat	blood
31	chr19:41272000-41276800	Weak transcription	Primary T cells from cord blood	blood
32	chr19:41272000-41279400	Weak transcription	Ovary	ovary
33	chr19:41272000-41280400	Weak transcription	NHEK	skin
34	chr19:41272000-41280600	Weak transcription	NH-A	brain
35	chr19:41272000-41281200	Weak transcription	Osteobl	bone
36	chr19:41272000-41282600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr19:41272000-41282600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr19:41272000-41282600	Weak transcription	Brain Angular Gyrus	brain
39	chr19:41272000-41282600	Weak transcription	HUVEC	blood vessel
40	chr19:41272000-41282800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr19:41272000-41282800	Weak transcription	Psoas Muscle	Psoas
42	chr19:41272000-41282800	Weak transcription	Small Intestine	intestine
43	chr19:41272000-41282800	Weak transcription	NHDF-Ad	bronchial
44	chr19:41272200-41274800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:41272200-41275600	Strong transcription	Placenta	Placenta
46	chr19:41272200-41276800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr19:41272200-41276800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr19:41272200-41277000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr19:41272200-41277000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr19:41272200-41280800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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