Variant report

Variant	rs923242
Chromosome Location	chr15:59470330-59470331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11632378	0.89[AFR][1000 genomes]
rs11637519	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11852281	0.88[ASN][1000 genomes]
rs11854052	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11854099	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11857218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11858347	0.88[ASN][1000 genomes]
rs12591296	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12916831	1.00[ASN][1000 genomes]
rs17190785	0.88[ASN][1000 genomes]
rs17269517	0.88[ASN][1000 genomes]
rs1872742	1.00[ASN][1000 genomes]
rs1967063	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1979552	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2087123	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2101394	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2306786	0.85[ASN][1000 genomes]
rs2306790	0.88[ASN][1000 genomes]
rs41505445	0.82[GIH][hapmap]
rs58124311	0.88[ASN][1000 genomes]
rs7165001	0.80[MEX][hapmap]
rs7182408	0.82[ASN][1000 genomes]
rs8036783	0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs8040100	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs931346	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1035868	chr15:59402426-59530594	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs923242	ZNF280D	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59436000-59473000	Weak transcription	Brain Germinal Matrix	brain
2	chr15:59437800-59484400	Weak transcription	Fetal Brain Male	brain
3	chr15:59445600-59479600	Weak transcription	Fetal Kidney	kidney
4	chr15:59451200-59473600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:59451400-59470400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:59451600-59474600	Weak transcription	Psoas Muscle	Psoas
7	chr15:59454000-59482000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:59454800-59471600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:59458600-59473800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr15:59461000-59474800	Strong transcription	Liver	Liver
11	chr15:59463200-59473000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:59463600-59471800	Weak transcription	Small Intestine	intestine
13	chr15:59464000-59472800	Weak transcription	Ovary	ovary
14	chr15:59464200-59470400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr15:59464200-59470800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:59464200-59471600	Weak transcription	Pancreas	Pancrea
17	chr15:59464200-59474000	Weak transcription	HepG2	liver
18	chr15:59464400-59496800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr15:59466800-59473200	Weak transcription	Primary B cells from cord blood	blood
20	chr15:59466800-59474200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr15:59467200-59470600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:59467200-59474000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:59467400-59470400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr15:59467600-59473600	Weak transcription	Colon Smooth Muscle	Colon
25	chr15:59467800-59473400	Strong transcription	Fetal Intestine Small	intestine
26	chr15:59467800-59473600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr15:59467800-59473800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr15:59467800-59479600	Weak transcription	Brain Angular Gyrus	brain
29	chr15:59467800-59523200	Weak transcription	Fetal Brain Female	brain
30	chr15:59468000-59470600	Weak transcription	Fetal Heart	heart
31	chr15:59468000-59474000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:59468000-59479800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr15:59468000-59480000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr15:59468200-59528600	Weak transcription	Stomach Mucosa	stomach
35	chr15:59468600-59472200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:59468600-59472800	Strong transcription	Osteobl	bone
37	chr15:59468600-59521400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr15:59468800-59470400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:59468800-59471800	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr15:59468800-59472400	Strong transcription	HUVEC	blood vessel
41	chr15:59468800-59473000	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr15:59468800-59473400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:59468800-59490800	Strong transcription	Duodenum Mucosa	Duodenum
44	chr15:59468800-59492600	Strong transcription	Fetal Intestine Large	intestine
45	chr15:59469000-59470400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr15:59469000-59471000	Strong transcription	Colonic Mucosa	Colon
47	chr15:59469000-59471400	Strong transcription	Left Ventricle	heart
48	chr15:59469000-59471600	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:59469000-59471800	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:59469000-59471800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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