Variant report

Variant	rs11634364
Chromosome Location	chr15:100261042-100261043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:100260861-100261105	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr15:100260789-100261054	Hela-S3	cervix:	n/a	n/a
3	SPI1	chr15:100260722-100261150	HL-60	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:100256741..100258686-chr15:100260565..100262777,2	MCF-7	breast:
2	chr15:100260912..100262587-chr15:100270840..100273775,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LYSMD4-1	chr15:100260989-100261171	NONHSAT050878

No data

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

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11247124	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.84[ASN][1000 genomes]
rs12185079	0.80[ASN][1000 genomes]
rs2123926	0.84[ASN][1000 genomes]
rs2603229	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11634364	MEF2A	cis	parietal	SCAN
rs11634364	MEF2A	cis	cerebellum	SCAN
rs11634364	LYSMD4	cis	parietal	SCAN

Chromatin state (count:112 , 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	chr15:100249600-100272800	Weak transcription	Small Intestine	intestine
3	chr15:100249800-100272200	Weak transcription	HUVEC	blood vessel
4	chr15:100251800-100261600	Weak transcription	NHEK	skin
5	chr15:100251800-100271800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:100252200-100271400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:100253000-100265000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:100253000-100271800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:100253200-100268400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:100253400-100261400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:100253400-100261400	Weak transcription	Pancreas	Pancrea
12	chr15:100253400-100261400	Weak transcription	HepG2	liver
13	chr15:100253400-100263600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:100253600-100267600	Weak transcription	Fetal Brain Female	brain
15	chr15:100253600-100268000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:100253600-100268000	Weak transcription	Brain Germinal Matrix	brain
17	chr15:100253600-100268200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr15:100253600-100272400	Weak transcription	Stomach Mucosa	stomach
19	chr15:100255400-100269000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr15:100255800-100268400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:100256000-100265000	Weak transcription	Hela-S3	cervix
22	chr15:100256800-100265200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:100257000-100268200	Weak transcription	Gastric	stomach
24	chr15:100257200-100261200	Flanking Active TSS	GM12878-XiMat	blood
25	chr15:100257200-100265000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:100257200-100267800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr15:100257200-100268400	Weak transcription	Liver	Liver
28	chr15:100257400-100262200	Weak transcription	Fetal Brain Male	brain
29	chr15:100257400-100265000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:100257600-100270400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr15:100257800-100261600	Enhancers	Fetal Muscle Leg	muscle
32	chr15:100257800-100267200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr15:100257800-100267600	Weak transcription	NHLF	lung
34	chr15:100258000-100261400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr15:100258000-100261400	Weak transcription	Right Atrium	heart
36	chr15:100258000-100265000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:100258000-100265000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:100258000-100265200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr15:100258000-100267800	Weak transcription	Ovary	ovary
40	chr15:100258000-100268000	Weak transcription	Brain Anterior Caudate	brain
41	chr15:100258000-100268200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:100258000-100268600	Weak transcription	Colonic Mucosa	Colon
43	chr15:100258000-100268600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr15:100258000-100272000	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr15:100258400-100268200	Weak transcription	Brain Angular Gyrus	brain
46	chr15:100258600-100261400	Weak transcription	Placenta	Placenta
47	chr15:100258600-100261400	Weak transcription	Right Ventricle	heart
48	chr15:100258600-100265000	Weak transcription	Fetal Intestine Large	intestine
49	chr15:100258600-100268400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:100258800-100261600	Enhancers	Primary B cells from peripheral blood	blood

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