Variant report

Variant	rs2388497
Chromosome Location	chr13:30714792-30714793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30702300..30704333-chr13:30714151..30716262,2	K562	blood:
2	chr13:30707361..30710289-chr13:30714464..30717739,4	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs471343	0.87[EUR][1000 genomes]
rs472327	0.86[EUR][1000 genomes]
rs473909	0.87[EUR][1000 genomes]
rs480097	0.86[EUR][1000 genomes]
rs482983	0.87[EUR][1000 genomes]
rs559122	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs589064	0.81[EUR][1000 genomes]
rs597794	0.84[EUR][1000 genomes]
rs613712	0.87[EUR][1000 genomes]
rs614220	0.86[EUR][1000 genomes]
rs614644	0.87[EUR][1000 genomes]
rs616352	0.87[EUR][1000 genomes]
rs643621	0.91[GIH][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs656305	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7323177	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7327238	0.87[EUR][1000 genomes]
rs750683	0.80[EUR][1000 genomes]
rs913902	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[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	nsv1040215	chr13:30621351-30741022	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541745	chr13:30621351-30741022	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv832572	chr13:30650005-30835256	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv981	chr13:30703159-30739838	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv1847946	chr13:30707385-30731192	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2388497	PDX1	cis	cerebellum	SCAN
rs2388497	BRCA2	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30700200-30717200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr13:30707800-30715200	Weak transcription	Dnd41	blood
3	chr13:30708800-30715600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr13:30708800-30716800	Weak transcription	Brain Anterior Caudate	brain
5	chr13:30709400-30715600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr13:30709600-30715200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr13:30712600-30715800	Weak transcription	NHDF-Ad	bronchial
8	chr13:30712600-30716000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr13:30712600-30717000	Weak transcription	Brain Angular Gyrus	brain
10	chr13:30712800-30715800	Weak transcription	Adipose Nuclei	Adipose
11	chr13:30712800-30715800	Weak transcription	Placenta	Placenta
12	chr13:30712800-30716600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:30712800-30716600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr13:30712800-30716600	Weak transcription	Fetal Lung	lung
15	chr13:30712800-30716800	Weak transcription	Lung	lung
16	chr13:30713000-30715400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr13:30713000-30716000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr13:30713000-30716000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr13:30713000-30716000	Weak transcription	Hela-S3	cervix
20	chr13:30713000-30716000	Weak transcription	HUVEC	blood vessel
21	chr13:30713000-30716200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr13:30713000-30716600	Weak transcription	A549	lung
23	chr13:30713400-30715200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr13:30714200-30714800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr13:30714400-30715200	Enhancers	GM12878-XiMat	blood
26	chr13:30714400-30716000	Enhancers	Spleen	Spleen
27	chr13:30714400-30718000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr13:30714600-30715000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr13:30714600-30717800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr13:30714600-30721800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links