Variant report

Variant	rs4561439
Chromosome Location	chr15:40858227-40858228
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GTF3C2	chr15:40856838-40858354	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40856304..40858832-chr15:40886132..40888060,2	K562	blood:
2	chr15:40857525..40859323-chr15:40878424..40880579,2	K562	blood:
3	chr15:40855657..40859262-chr15:40860971..40863634,5	MCF-7	breast:
4	chr15:40856363..40858923-chr15:41165345..41167356,2	K562	blood:

Variant related genes	Relation type
RPUSD2	TF binding region
C15orf57	TF binding region
ENSG00000137812	Chromatin interaction
ENSG00000166133	Chromatin interaction
ENSG00000104140	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10444792	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10518696	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10851397	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11070276	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11070278	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11632319	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11637275	0.86[AFR][1000 genomes]
rs12442697	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12916218	1.00[CEU][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1453182	1.00[CEU][hapmap]
rs1530942	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1530943	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16970734	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16970854	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1801320	1.00[CEU][hapmap]
rs1869303	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1987795	0.91[AMR][1000 genomes]
rs2014367	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2034653	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2278887	0.92[ASN][1000 genomes]
rs2278889	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2290379	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2304579	1.00[CEU][hapmap]
rs2412528	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2412530	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2412533	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2924389	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2959535	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2959547	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3803354	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4467046	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4923873	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4923877	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4923878	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4923879	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4924473	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4924474	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4924476	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4924482	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924483	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57140606	0.96[EUR][1000 genomes]
rs57736474	0.94[EUR][1000 genomes]
rs58458955	0.82[EUR][1000 genomes]
rs589650	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59654927	0.82[EUR][1000 genomes]
rs607118	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61381741	0.82[EUR][1000 genomes]
rs617031	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs623187	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs624486	0.81[EUR][1000 genomes]
rs640919	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6492952	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6492953	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6492955	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7163648	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7163889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7164166	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7164405	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167239	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7167922	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7168913	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7168927	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7170073	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7170327	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7170946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73396510	0.94[EUR][1000 genomes]
rs73396515	0.94[EUR][1000 genomes]
rs8024579	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8024802	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8029208	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8032453	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8033739	0.92[EUR][1000 genomes]
rs8034726	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8035774	0.81[AFR][1000 genomes]
rs8038350	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8040187	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8041816	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8041991	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8043197	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs896797	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs921624	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9284288	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs976402	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9783737	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4561439	C15orf57	cis	Whole Blood	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40856600-40858400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr15:40857200-40859200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:40857200-40861200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:40857400-40860800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:40857600-40860800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:40857800-40858400	Enhancers	Fetal Heart	heart
7	chr15:40857800-40858800	Enhancers	Placenta	Placenta
8	chr15:40857800-40859000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:40857800-40859200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:40857800-40859600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:40857800-40860600	Weak transcription	Brain Angular Gyrus	brain
12	chr15:40857800-40860800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:40857800-40860800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:40857800-40860800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:40857800-40860800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:40857800-40860800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:40857800-40860800	Weak transcription	Colon Smooth Muscle	Colon
18	chr15:40857800-40860800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr15:40857800-40860800	Weak transcription	Fetal Lung	lung
20	chr15:40857800-40860800	Weak transcription	Stomach Mucosa	stomach
21	chr15:40857800-40860800	Weak transcription	NHLF	lung
22	chr15:40857800-40860800	Weak transcription	Osteobl	bone
23	chr15:40857800-40861000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:40857800-40861000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:40857800-40861000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:40857800-40861000	Weak transcription	HSMM	muscle
27	chr15:40857800-40861000	Weak transcription	HSMMtube	muscle
28	chr15:40857800-40861200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:40857800-40861200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:40858000-40858400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr15:40858000-40858400	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr15:40858000-40858800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:40858000-40859200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr15:40858000-40859200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr15:40858000-40859200	Weak transcription	Liver	Liver
36	chr15:40858000-40859400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr15:40858000-40859400	Weak transcription	Brain Substantia Nigra	brain
38	chr15:40858000-40860000	Enhancers	K562	blood
39	chr15:40858000-40860600	Weak transcription	Primary T cells from cord blood	blood
40	chr15:40858000-40860600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr15:40858000-40860600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:40858000-40860600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr15:40858000-40860600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:40858000-40860600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:40858000-40860600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr15:40858000-40860600	Weak transcription	Brain Anterior Caudate	brain
47	chr15:40858000-40860600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr15:40858000-40860600	Weak transcription	Brain Germinal Matrix	brain
49	chr15:40858000-40860600	Weak transcription	Brain Hippocampus Middle	brain
50	chr15:40858000-40860600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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