Variant report

Variant	rs4924495
Chromosome Location	chr15:40993710-40993711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40992580..40995462-chr15:41019256..41021826,2	K562	blood:
2	chr15:40986558..40989601-chr15:40990368..40993764,9	K562	blood:

Variant related genes	Relation type
ENSG00000051180	Chromatin interaction
ENSG00000245849	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10775121	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11070291	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11070293	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11631563	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11633269	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11852786	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11855560	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11858337	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11858338	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12372947	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12439683	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12441514	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12442845	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12593359	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12908284	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12912742	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2263551	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304582	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2412546	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2412547	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2412548	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2412549	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2577564	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2619679	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2619680	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2619683	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2917955	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2928140	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3092982	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3092983	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3101861	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34400306	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36106105	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs45495293	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4923884	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924493	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924501	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924503	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56042757	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6492961	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7164339	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7167854	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7169010	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7172195	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7173646	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7174551	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7175401	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs752012	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8025883	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8033829	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8036817	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv529030	chr15:40956471-41012695	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv904100	chr15:40959624-40994706	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
10	nsv527234	chr15:40987725-41031686	Transcr. at gene 5' and 3' Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4924495	C15orf57	cis	Adipose Subcutaneous	GTEx
rs4924495	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs4924495	CCDC32	cis	multi-tissue	Pritchard
rs4924495	RAD51	cis	multi-tissue	Pritchard
rs4924495	C15orf57	cis	Artery Tibial	GTEx
rs4924495	RP11-111A22.1	cis	lung	GTEx
rs4924495	C15orf57	cis	Nerve Tibial	GTEx
rs4924495	C15orf57	cis	lung	GTEx
rs4924495	RP11-111A22.1	cis	Artery Tibial	GTEx
rs4924495	CCDC32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40988000-40999400	Weak transcription	Right Atrium	heart
2	chr15:40988000-41030000	Weak transcription	Pancreas	Pancrea
3	chr15:40988200-41001200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:40988200-41028600	Weak transcription	Spleen	Spleen
5	chr15:40988400-40998000	Weak transcription	Fetal Intestine Large	intestine
6	chr15:40988400-41020600	Weak transcription	Placenta	Placenta
7	chr15:40988400-41020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:40988400-41021600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr15:40988400-41021800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:40988400-41027200	Weak transcription	Primary B cells from cord blood	blood
11	chr15:40988400-41031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr15:40988600-40994800	Weak transcription	Fetal Intestine Small	intestine
13	chr15:40988600-40998400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:40988600-41000800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr15:40988600-41001200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:40988600-41007800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr15:40988600-41018400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:40988600-41021400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr15:40988600-41021400	Weak transcription	Fetal Brain Female	brain
20	chr15:40988800-40998600	Weak transcription	Gastric	stomach
21	chr15:40988800-40998600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr15:40988800-41000800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:40988800-41000800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:40988800-41000800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:40988800-41001200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:40988800-41002800	Weak transcription	Brain Germinal Matrix	brain
27	chr15:40988800-41020600	Weak transcription	Primary T cells from cord blood	blood
28	chr15:40988800-41021600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:40988800-41021800	Weak transcription	Fetal Kidney	kidney
30	chr15:40989000-41001000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:40989000-41001200	Weak transcription	Fetal Lung	lung
32	chr15:40989000-41012000	Weak transcription	NHLF	lung
33	chr15:40989000-41018000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:40989200-40997200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr15:40989200-40997200	Weak transcription	NHEK	skin
36	chr15:40989200-40998000	Weak transcription	Fetal Heart	heart
37	chr15:40989200-41001200	Weak transcription	A549	lung
38	chr15:40989200-41002800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr15:40990000-41004800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr15:40990200-40999400	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:40990200-41006800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:40990200-41013200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr15:40990200-41016800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:40990200-41016800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:40990400-40994600	Weak transcription	GM12878-XiMat	blood
46	chr15:40990600-41015000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:40990600-41022600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:40990800-40993800	Strong transcription	Hela-S3	cervix
49	chr15:40990800-40994000	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr15:40990800-40994600	Strong transcription	Monocytes-CD14+_RO01746	blood

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