Variant report

Variant	rs2959545
Chromosome Location	chr15:40804071-40804072
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40768530..40771380-chr15:40802476..40804326,2	K562	blood:
2	chr15:40802752..40805307-chr15:40819242..40820883,2	K562	blood:
3	chr15:40789702..40793899-chr15:40802454..40805435,6	K562	blood:
4	chr15:40797459..40799431-chr15:40802673..40805643,2	K562	blood:
5	chr15:40803911..40804534-chr15:40811594..40812575,2	K562	blood:
6	chr15:40730812..40733256-chr15:40803333..40806622,3	K562	blood:
7	chr15:40762122..40764569-chr15:40802898..40805797,2	MCF-7	breast:
8	chr15:40790726..40793810-chr15:40802454..40804415,3	K562	blood:
9	chr15:40730812..40737363-chr15:40801226..40806622,9	K562	blood:
10	chr15:40800305..40802269-chr15:40802285..40805070,2	K562	blood:
11	chr15:40801534..40804191-chr15:40830855..40832642,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000140320	Chromatin interaction
ENSG00000169105	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11070275	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11070277	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11632061	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11632370	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11638742	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11639464	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12594548	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12595610	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12916042	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1806961	0.90[EUR][1000 genomes]
rs1811513	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1813898	0.81[EUR][1000 genomes]
rs1869301	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1869302	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1993212	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2034651	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2034652	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2167795	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2412531	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2412532	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2412534	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2444302	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2924386	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2924388	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2959536	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4923875	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4923876	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4924472	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924478	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4924479	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4924480	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4924481	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs588686	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs590046	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs603623	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs616937	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs618399	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs619711	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs620198	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6492951	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs654317	0.82[EUR][1000 genomes]
rs6582	0.81[EUR][1000 genomes]
rs7178756	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7183273	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7494968	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8029384	0.81[EUR][1000 genomes]
rs896795	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9652415	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs976401	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2959545	C15orf57	cis	Adipose Subcutaneous	GTEx
rs2959545	RP11-111A22.1	cis	Artery Tibial	GTEx
rs2959545	C15orf57	cis	Artery Tibial	GTEx
rs2959545	RP11-111A22.1	cis	lung	GTEx
rs2959545	C15orf57	cis	lung	GTEx
rs2959545	C15orf57	cis	Nerve Tibial	GTEx
rs2959545	C15orf57	cis	Heart Left Ventricle	GTEx
rs2959545	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs2959545	C15orf57	cis	Esophagus Muscularis	GTEx
rs2959545	CCDC32	cis	multi-tissue	Pritchard
rs2959545	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs2959545	C15orf57	cis	Muscle Skeletal	GTEx
rs2959545	RP11-111A22.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40802800-40804200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:40803000-40804200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
3	chr15:40803200-40804200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
4	chr15:40803200-40804200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
5	chr15:40803200-40804200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:40803200-40804200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
7	chr15:40803200-40804400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr15:40803200-40804400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr15:40803200-40804400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:40803200-40804400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:40803200-40804400	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr15:40803200-40804400	Active TSS	Brain Angular Gyrus	brain
13	chr15:40803200-40804400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
14	chr15:40803200-40804400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
15	chr15:40803200-40804600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr15:40803200-40804600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:40803200-40804600	Active TSS	Rectal Smooth Muscle	rectum
18	chr15:40803200-40804600	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr15:40803400-40804200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr15:40803400-40804200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:40803400-40804200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr15:40803400-40804200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:40803400-40804200	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr15:40803400-40804200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
25	chr15:40803400-40804200	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr15:40803400-40804200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
27	chr15:40803400-40804200	Active TSS	Brain Hippocampus Middle	brain
28	chr15:40803400-40804200	Active TSS	Left Ventricle	heart
29	chr15:40803400-40804200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
30	chr15:40803400-40804200	Active TSS	Psoas Muscle	Psoas
31	chr15:40803400-40804200	Bivalent/Poised TSS	Stomach Mucosa	stomach
32	chr15:40803400-40804200	Flanking Bivalent TSS/Enh	Thymus	Thymus
33	chr15:40803400-40804200	Active TSS	NHLF	lung
34	chr15:40803400-40804400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
35	chr15:40803400-40804400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
36	chr15:40803400-40804400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:40803400-40804400	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr15:40803400-40804400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
39	chr15:40803400-40804400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
40	chr15:40803400-40804400	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr15:40803400-40804400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr15:40803400-40804400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:40803400-40804400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
44	chr15:40803400-40804400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
45	chr15:40803400-40804400	Active TSS	Brain Substantia Nigra	brain
46	chr15:40803400-40804400	Flanking Active TSS	Colonic Mucosa	Colon
47	chr15:40803400-40804400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
48	chr15:40803400-40804400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
49	chr15:40803400-40804400	Flanking Active TSS	Pancreas	Pancrea
50	chr15:40803400-40804400	Active TSS	HSMMtube	muscle

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