Variant report

Variant	rs325403
Chromosome Location	chr15:100251015-100251016
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:100249685..100254377-chr15:100271525..100276233,5	MCF-7	breast:
2	chr15:100249823..100251812-chr15:100273635..100275364,2	MCF-7	breast:
3	chr15:100250161..100251690-chr15:100252996..100255085,2	K562	blood:
4	chr15:100249762..100251661-chr15:100253585..100255410,2	K562	blood:

Variant related genes	Relation type
ENSG00000183060	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2123930	0.89[CHD][hapmap]
rs2570817	0.84[CHD][hapmap]
rs2570930	0.87[CHD][hapmap]
rs2570934	0.82[CHD][hapmap]
rs325384	0.80[ASN][1000 genomes]
rs325386	0.80[ASN][1000 genomes]
rs325389	0.81[ASN][1000 genomes]
rs325393	0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs325397	0.80[ASN][1000 genomes]
rs325412	0.83[ASN][1000 genomes]
rs325415	0.81[ASN][1000 genomes]
rs8029296	0.80[ASN][1000 genomes]
rs8034889	0.89[CHD][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv904559	chr15:100174907-100255046	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs325403	MEF2A	cis	cerebellum	SCAN
rs325403	LYSMD4	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100159000-100253000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:100233400-100251200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:100233800-100256600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:100244600-100252800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:100244600-100254800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:100244600-100272400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:100245000-100251600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:100245000-100258200	Weak transcription	Fetal Kidney	kidney
9	chr15:100245600-100256200	Strong transcription	Dnd41	blood
10	chr15:100245600-100258000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:100246200-100257000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr15:100246400-100253600	Strong transcription	Primary hematopoietic stem cells	blood
13	chr15:100246400-100256400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr15:100246400-100257400	Strong transcription	Primary B cells from cord blood	blood
15	chr15:100246600-100257400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:100246800-100259000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:100247000-100252800	Genic enhancers	Fetal Muscle Leg	muscle
18	chr15:100247000-100258600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:100247200-100256800	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr15:100248400-100253400	Strong transcription	HepG2	liver
21	chr15:100248400-100256400	Strong transcription	GM12878-XiMat	blood
22	chr15:100248400-100259600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:100248400-100260000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:100248800-100258000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:100249000-100259600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr15:100249200-100251200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:100249200-100252600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
28	chr15:100249200-100253800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr15:100249200-100257200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:100249200-100257200	Strong transcription	Thymus	Thymus
31	chr15:100249200-100259600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr15:100249400-100251400	Strong transcription	Fetal Stomach	stomach
33	chr15:100249400-100252600	Strong transcription	Fetal Thymus	thymus
34	chr15:100249400-100257000	Weak transcription	Fetal Brain Male	brain
35	chr15:100249400-100258600	Strong transcription	Fetal Intestine Large	intestine
36	chr15:100249400-100260200	Weak transcription	A549	lung
37	chr15:100249600-100251200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:100249600-100252800	Genic enhancers	Stomach Smooth Muscle	stomach
39	chr15:100249600-100253600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr15:100249600-100257200	Strong transcription	Liver	Liver
41	chr15:100249600-100258600	Strong transcription	Primary T cells from cord blood	blood
42	chr15:100249600-100272800	Weak transcription	Small Intestine	intestine
43	chr15:100249800-100251200	Weak transcription	Brain Angular Gyrus	brain
44	chr15:100249800-100251200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr15:100249800-100251200	Strong transcription	Lung	lung
46	chr15:100249800-100251200	Weak transcription	Right Atrium	heart
47	chr15:100249800-100251800	Strong transcription	HSMM	muscle
48	chr15:100249800-100252000	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr15:100249800-100252600	Weak transcription	Psoas Muscle	Psoas
50	chr15:100249800-100252600	Genic enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links