Variant report

Variant	rs7170288
Chromosome Location	chr15:40858818-40858819
allele	A/G
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	MAX	chr15:40858776-40859299	K562	blood:	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
C15orf57	TF binding region
RPUSD2	TF binding region
ENSG00000104140	Chromatin interaction
ENSG00000137812	Chromatin interaction
ENSG00000166133	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10152546	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1044474	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10518697	0.92[EUR][1000 genomes]
rs1058734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070283	0.91[EUR][1000 genomes]
rs11630273	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11633184	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11637245	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11637422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324748	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12385982	0.91[EUR][1000 genomes]
rs12441754	0.83[EUR][1000 genomes]
rs12903817	0.87[EUR][1000 genomes]
rs12908316	0.89[EUR][1000 genomes]
rs12913296	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12913739	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12915171	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915636	0.92[EUR][1000 genomes]
rs13329076	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17673703	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17674454	0.91[EUR][1000 genomes]
rs17747423	0.92[EUR][1000 genomes]
rs17747633	0.92[EUR][1000 genomes]
rs1814541	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1814542	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2412525	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28634695	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28647196	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28669075	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34739056	0.82[EUR][1000 genomes]
rs34824658	0.88[EUR][1000 genomes]
rs35127391	0.92[EUR][1000 genomes]
rs35684277	0.86[EUR][1000 genomes]
rs35842610	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4923880	0.90[EUR][1000 genomes]
rs4924486	0.90[EUR][1000 genomes]
rs62019876	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62019879	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71471880	0.86[EUR][1000 genomes]
rs7165509	0.86[EUR][1000 genomes]
rs7175747	0.85[EUR][1000 genomes]
rs8029530	0.82[EUR][1000 genomes]
rs8036891	0.82[EUR][1000 genomes]
rs8037180	0.84[EUR][1000 genomes]
rs8038122	0.86[EUR][1000 genomes]
rs8042386	0.84[EUR][1000 genomes]
rs9920642	0.86[EUR][1000 genomes]
rs9920676	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:21)

SNP	Gene	Cis/trans	Tissue	Source
rs7170288	C15orf57	cis	Esophagus Muscularis	GTEx
rs7170288	RP11-111A22.1	cis	Artery Tibial	GTEx
rs7170288	C15orf57	cis	lung	GTEx
rs7170288	RAD51	cis	multi-tissue	Pritchard
rs7170288	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs7170288	RP11-111A22.1	cis	Stomach	GTEx
rs7170288	RP11-111A22.1	cis	Artery Aorta	GTEx
rs7170288	C15orf57	cis	Stomach	GTEx
rs7170288	RP11-111A22.1	cis	lung	GTEx
rs7170288	C15orf57	cis	Muscle Skeletal	GTEx
rs7170288	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs7170288	C15orf57	cis	Adipose Subcutaneous	GTEx
rs7170288	C15orf57	cis	Artery Tibial	GTEx
rs7170288	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs7170288	C15orf57	cis	Artery Aorta	GTEx
rs7170288	CCDC32	cis	multi-tissue	Pritchard
rs7170288	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs7170288	C15orf57	cis	Heart Left Ventricle	GTEx
rs7170288	C15orf57	cis	Nerve Tibial	GTEx
rs7170288	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs7170288	C15orf57	cis	Esophagus Mucosa	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40857200-40859200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr15:40857200-40861200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:40857400-40860800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:40857600-40860800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:40857800-40859000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:40857800-40859200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:40857800-40859600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:40857800-40860600	Weak transcription	Brain Angular Gyrus	brain
9	chr15:40857800-40860800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:40857800-40860800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:40857800-40860800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:40857800-40860800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr15:40857800-40860800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:40857800-40860800	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:40857800-40860800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr15:40857800-40860800	Weak transcription	Fetal Lung	lung
17	chr15:40857800-40860800	Weak transcription	Stomach Mucosa	stomach
18	chr15:40857800-40860800	Weak transcription	NHLF	lung
19	chr15:40857800-40860800	Weak transcription	Osteobl	bone
20	chr15:40857800-40861000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:40857800-40861000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:40857800-40861000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:40857800-40861000	Weak transcription	HSMM	muscle
24	chr15:40857800-40861000	Weak transcription	HSMMtube	muscle
25	chr15:40857800-40861200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr15:40857800-40861200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:40858000-40859200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr15:40858000-40859200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:40858000-40859200	Weak transcription	Liver	Liver
30	chr15:40858000-40859400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:40858000-40859400	Weak transcription	Brain Substantia Nigra	brain
32	chr15:40858000-40860000	Enhancers	K562	blood
33	chr15:40858000-40860600	Weak transcription	Primary T cells from cord blood	blood
34	chr15:40858000-40860600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:40858000-40860600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:40858000-40860600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr15:40858000-40860600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr15:40858000-40860600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr15:40858000-40860600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr15:40858000-40860600	Weak transcription	Brain Anterior Caudate	brain
41	chr15:40858000-40860600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr15:40858000-40860600	Weak transcription	Brain Germinal Matrix	brain
43	chr15:40858000-40860600	Weak transcription	Brain Hippocampus Middle	brain
44	chr15:40858000-40860600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:40858000-40860600	Weak transcription	Fetal Muscle Leg	muscle
46	chr15:40858000-40860600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:40858000-40860600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr15:40858000-40860600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr15:40858000-40860600	Weak transcription	A549	lung
50	chr15:40858000-40860600	Weak transcription	GM12878-XiMat	blood

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