Variant report

Variant	rs325400
Chromosome Location	chr15:100252805-100252806
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:100251559..100254506-chr15:100254919..100256513,2	MCF-7	breast:
2	chr15:100249685..100254377-chr15:100271525..100276233,5	MCF-7	breast:
3	chr15:99826754..99827284-chr15:100252329..100253288,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183060	Chromatin interaction
ENSG00000168904	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11631947	0.84[JPT][hapmap]
rs12438623	0.84[JPT][hapmap]
rs1991921	0.84[JPT][hapmap]
rs325380	0.84[JPT][hapmap]
rs4965260	0.84[JPT][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs325400	MEF2A	cis	cerebellum	SCAN
rs325400	LYSMD4	cis	parietal	SCAN
rs325400	SPATA8	cis	cerebellum	SCAN
rs325400	LYSMD4	cis	cerebellum	SCAN
rs325400	LYSMD4	cis	Thyroid	GTEx

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	chr15:100233800-100256600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr15:100244600-100254800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:100244600-100272400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:100245000-100258200	Weak transcription	Fetal Kidney	kidney
6	chr15:100245600-100256200	Strong transcription	Dnd41	blood
7	chr15:100245600-100258000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr15:100246200-100257000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr15:100246400-100253600	Strong transcription	Primary hematopoietic stem cells	blood
10	chr15:100246400-100256400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr15:100246400-100257400	Strong transcription	Primary B cells from cord blood	blood
12	chr15:100246600-100257400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr15:100246800-100259000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:100247000-100258600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:100247200-100256800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr15:100248400-100253400	Strong transcription	HepG2	liver
17	chr15:100248400-100256400	Strong transcription	GM12878-XiMat	blood
18	chr15:100248400-100259600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:100248400-100260000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:100248800-100258000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:100249000-100259600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr15:100249200-100253800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr15:100249200-100257200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:100249200-100257200	Strong transcription	Thymus	Thymus
25	chr15:100249200-100259600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr15:100249400-100257000	Weak transcription	Fetal Brain Male	brain
27	chr15:100249400-100258600	Strong transcription	Fetal Intestine Large	intestine
28	chr15:100249400-100260200	Weak transcription	A549	lung
29	chr15:100249600-100253600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr15:100249600-100257200	Strong transcription	Liver	Liver
31	chr15:100249600-100258600	Strong transcription	Primary T cells from cord blood	blood
32	chr15:100249600-100272800	Weak transcription	Small Intestine	intestine
33	chr15:100249800-100253600	Strong transcription	Spleen	Spleen
34	chr15:100249800-100272200	Weak transcription	HUVEC	blood vessel
35	chr15:100250000-100253000	Genic enhancers	Right Ventricle	heart
36	chr15:100250000-100253200	Genic enhancers	Fetal Heart	heart
37	chr15:100250000-100253400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:100250000-100253600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:100250000-100255400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:100250000-100255400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr15:100250200-100253600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:100250200-100254200	Strong transcription	NHLF	lung
43	chr15:100250200-100256400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:100250400-100254600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:100250600-100253000	Strong transcription	Fetal Intestine Small	intestine
46	chr15:100250600-100253200	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr15:100250600-100253400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:100250600-100253600	Strong transcription	Fetal Lung	lung
49	chr15:100250600-100253600	Strong transcription	Osteobl	bone
50	chr15:100250600-100256000	Strong transcription	NH-A	brain

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