Variant report

Variant	rs11247123
Chromosome Location	chr15:100258980-100258981
allele	G/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	POLR2A	chr15:100256616-100259014	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr15:100258924-100259375	HepG2	liver:	n/a	n/a
3	IKZF1	chr15:100258773-100259851	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:100256683-100259904	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:100258853-100259031	MCF10A-Er-Src	breast:	n/a	n/a
6	MTA3	chr15:100258860-100259743	GM12878	blood:	n/a	n/a
7	RUNX3	chr15:100258744-100259893	GM12878	blood:	n/a	n/a
8	RELA	chr15:100258780-100259987	GM19099	blood:	n/a	n/a
9	POLR2A	chr15:100258880-100259966	HepG2	liver:	n/a	n/a
10	RUNX3	chr15:100257685-100260095	GM12878	blood:	n/a	n/a
11	PML	chr15:100258797-100260183	GM12878	blood:	n/a	n/a
12	MTA3	chr15:100258825-100260108	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:100257917..100259969-chr15:100273281..100275251,2	MCF-7	breast:
2	chr15:100104819..100107629-chr15:100257615..100260464,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214397	TF binding region
ENSG00000068305	Chromatin interaction
ENSG00000183060	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1808723	0.85[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2061007	0.96[CEU][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2123927	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2603221	0.88[ASN][1000 genomes]
rs2862867	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs325380	0.89[CEU][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs882175	0.84[ASN][1000 genomes]
rs882176	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs921704	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1038005	chr15:100170414-100633714	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv542522	chr15:100170414-100633714	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv904560	chr15:100196657-100339331	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv904561	chr15:100204918-100486828	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv428313	chr15:100236203-100757039	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv904563	chr15:100239546-100274747	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv570730	chr15:100240910-100700520	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv1045838	chr15:100243067-101032218	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv904564	chr15:100245296-100723798	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
13	nsv932678	chr15:100250311-101012358	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11247123	LYSMD4	cis	parietal	SCAN
rs11247123	LYSMD4	cis	cerebellum	SCAN
rs11247123	MEF2A	cis	cerebellum	SCAN
rs11247123	LYSMD4	cis	Thyroid	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100244600-100272400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:100246800-100259000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:100248400-100259600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:100248400-100260000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:100249000-100259600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:100249200-100259600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:100249400-100260200	Weak transcription	A549	lung
8	chr15:100249600-100272800	Weak transcription	Small Intestine	intestine
9	chr15:100249800-100272200	Weak transcription	HUVEC	blood vessel
10	chr15:100251800-100261600	Weak transcription	NHEK	skin
11	chr15:100251800-100271800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:100252200-100271400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:100252600-100260800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:100253000-100259800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr15:100253000-100260800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:100253000-100261000	Weak transcription	Esophagus	oesophagus
17	chr15:100253000-100265000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:100253000-100271800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr15:100253200-100260800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:100253200-100268400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:100253400-100260200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr15:100253400-100261400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:100253400-100261400	Weak transcription	Pancreas	Pancrea
24	chr15:100253400-100261400	Weak transcription	HepG2	liver
25	chr15:100253400-100263600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:100253600-100259200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr15:100253600-100259600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr15:100253600-100259600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr15:100253600-100259600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr15:100253600-100267600	Weak transcription	Fetal Brain Female	brain
31	chr15:100253600-100268000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:100253600-100268000	Weak transcription	Brain Germinal Matrix	brain
33	chr15:100253600-100268200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr15:100253600-100272400	Weak transcription	Stomach Mucosa	stomach
35	chr15:100254400-100259200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr15:100255400-100259600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:100255400-100269000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr15:100255600-100259000	Genic enhancers	Fetal Stomach	stomach
39	chr15:100255800-100268400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr15:100256000-100260800	Weak transcription	Spleen	Spleen
41	chr15:100256000-100265000	Weak transcription	Hela-S3	cervix
42	chr15:100256200-100259400	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr15:100256200-100259800	Weak transcription	Dnd41	blood
44	chr15:100256600-100260000	Enhancers	Psoas Muscle	Psoas
45	chr15:100256800-100259200	Enhancers	Fetal Lung	lung
46	chr15:100256800-100260000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:100256800-100260000	Enhancers	HSMMtube	muscle
48	chr15:100256800-100260600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr15:100256800-100265200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:100257000-100259200	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links