Variant report

Variant	rs4924390
Chromosome Location	chr15:40064229-40064230
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40064104..40066039-chr15:40073155..40075759,2	K562	blood:

Variant related genes	Relation type
ENSG00000261136	Chromatin interaction
ENSG00000150667	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1021410	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1021411	0.84[CEU][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1027232	0.80[CHB][hapmap]
rs11858148	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs12437837	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs12440567	0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs1491624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1565559	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1565561	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16969789	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs16969802	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs1844863	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1906166	0.81[ASN][1000 genomes]
rs2029584	0.80[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2171312	0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs2631717	0.81[ASN][1000 genomes]
rs28450006	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28538495	0.85[ASN][1000 genomes]
rs28884199	0.85[ASN][1000 genomes]
rs28896916	0.85[ASN][1000 genomes]
rs34320375	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35652496	0.98[ASN][1000 genomes]
rs4924387	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs4924388	0.85[ASN][1000 genomes]
rs4924392	0.86[ASN][1000 genomes]
rs55639610	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59434895	0.83[ASN][1000 genomes]
rs60431166	0.83[ASN][1000 genomes]
rs61695850	0.83[ASN][1000 genomes]
rs62004808	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179742	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179838	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180846	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026892	0.82[ASN][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	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4924390	C15orf54	cis	cerebellum	SCAN
rs4924390	RPAP1	cis	parietal	SCAN
rs4924390	ACTC1	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40053400-40069400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:40054400-40069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:40059400-40074400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:40063000-40064400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:40063000-40064400	Enhancers	Fetal Stomach	stomach
6	chr15:40063000-40064600	Enhancers	Fetal Muscle Leg	muscle
7	chr15:40063200-40064400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:40063200-40064400	Enhancers	Colon Smooth Muscle	Colon
9	chr15:40063200-40064400	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr15:40063200-40066600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:40063400-40064400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:40063400-40064400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:40063400-40064400	Flanking Active TSS	Osteobl	bone
14	chr15:40063600-40064400	Enhancers	Lung	lung
15	chr15:40063800-40064400	Enhancers	Adipose Nuclei	Adipose
16	chr15:40063800-40064600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:40063800-40065800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:40063800-40066600	Weak transcription	GM12878-XiMat	blood
19	chr15:40063800-40067800	Weak transcription	Esophagus	oesophagus
20	chr15:40063800-40068800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:40063800-40068800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr15:40063800-40069000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:40063800-40074000	Weak transcription	Brain Angular Gyrus	brain
24	chr15:40064000-40064400	Enhancers	Brain Substantia Nigra	brain
25	chr15:40064000-40064400	Enhancers	NH-A	brain
26	chr15:40064000-40064400	Flanking Active TSS	NHDF-Ad	bronchial
27	chr15:40064000-40066800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr15:40064000-40069400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:40064000-40074000	Weak transcription	Brain Anterior Caudate	brain
30	chr15:40064200-40064400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:40064200-40064400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:40064200-40064400	Enhancers	Rectal Smooth Muscle	rectum
33	chr15:40064200-40064400	Enhancers	Stomach Smooth Muscle	stomach
34	chr15:40064200-40064400	Enhancers	HSMMtube	muscle
35	chr15:40064200-40064400	Enhancers	NHLF	lung
36	chr15:40064200-40064600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:40064200-40064600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:40064200-40064600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr15:40064200-40064600	Enhancers	HSMM	muscle
40	chr15:40064200-40073800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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