Variant report

Variant	rs10152546
Chromosome Location	chr15:40855210-40855211
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr15:40854853-40855386	T-47D	breast:	n/a	n/a
2	GATA3	chr15:40854886-40855381	T-47D	breast:	n/a	n/a
3	GATA3	chr15:40854907-40855329	T-47D	breast:	n/a	n/a
4	EP300	chr15:40854913-40855353	T-47D	breast:	n/a	n/a
5	FOXA1	chr15:40854863-40855270	T-47D	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40854296..40857804-chr15:40884735..40887632,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM82A2-5	chr15:40854971-40855226	NONHSAT041858

No data

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

Extended variants
information (count: 62 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1044474	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10518697	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs1058734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11070283	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs11630273	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11633184	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11637245	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11637422	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12148915	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12324748	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12385982	0.89[EUR][1000 genomes]
rs12441754	0.81[EUR][1000 genomes]
rs12592524	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12903817	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12908316	0.87[EUR][1000 genomes]
rs12913296	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12913739	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12915171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12915636	0.90[EUR][1000 genomes]
rs13329076	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16970758	0.90[YRI][hapmap]
rs17673703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17674454	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs17747423	0.90[EUR][1000 genomes]
rs17747633	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs1801321	0.92[CEU][hapmap]
rs1814541	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2053973	0.95[YRI][hapmap]
rs2412525	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28634695	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28647196	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28669075	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34739056	0.80[EUR][1000 genomes]
rs34824658	0.86[EUR][1000 genomes]
rs35127391	0.92[EUR][1000 genomes]
rs35684277	0.84[EUR][1000 genomes]
rs35842610	0.93[EUR][1000 genomes]
rs4923880	0.88[EUR][1000 genomes]
rs4924486	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs4924496	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62019876	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62019879	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6492964	0.84[CEU][hapmap]
rs71471880	0.84[EUR][1000 genomes]
rs7165509	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7170288	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7175747	0.83[EUR][1000 genomes]
rs7177265	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7180135	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8029530	0.80[EUR][1000 genomes]
rs8036891	0.80[EUR][1000 genomes]
rs8037180	0.82[EUR][1000 genomes]
rs8038122	0.84[EUR][1000 genomes]
rs8042386	0.82[EUR][1000 genomes]
rs957603	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9920642	0.84[EUR][1000 genomes]
rs9920676	0.90[EUR][1000 genomes]
rs999197	0.87[YRI][hapmap]

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:23)

SNP	Gene	Cis/trans	Tissue	Source
rs10152546	C15orf57	cis	Muscle Skeletal	GTEx
rs10152546	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs10152546	C15orf57	cis	Esophagus Mucosa	GTEx
rs10152546	RP11-111A22.1	cis	Artery Aorta	GTEx
rs10152546	C15orf57	cis	Heart Left Ventricle	GTEx
rs10152546	C15orf57	cis	Stomach	GTEx
rs10152546	CCDC32	cis	lesional skin	skin_eQTL
rs10152546	RP11-111A22.1	cis	Artery Tibial	GTEx
rs10152546	C15orf57	cis	Esophagus Muscularis	GTEx
rs10152546	CCDC32	cis	normal skin	skin_eQTL
rs10152546	CCDC32	cis	uninvolved skin	skin_eQTL
rs10152546	RAD51	cis	multi-tissue	Pritchard
rs10152546	C15orf57	cis	Adipose Subcutaneous	GTEx
rs10152546	C15orf57	cis	Artery Tibial	GTEx
rs10152546	C15orf57	cis	Artery Aorta	GTEx
rs10152546	RP11-111A22.1	cis	lung	GTEx
rs10152546	C15orf57	cis	lung	GTEx
rs10152546	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs10152546	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs10152546	CCDC32	cis	multi-tissue	Pritchard
rs10152546	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs10152546	C15orf57	cis	Nerve Tibial	GTEx
rs10152546	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40821800-40856400	Weak transcription	Colon Smooth Muscle	Colon
2	chr15:40822600-40856400	Weak transcription	Small Intestine	intestine
3	chr15:40828000-40856600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:40831600-40856600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:40838000-40856400	Weak transcription	A549	lung
6	chr15:40838600-40855600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr15:40840000-40856400	Weak transcription	Fetal Brain Female	brain
8	chr15:40840000-40856600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:40842400-40856200	Weak transcription	Colonic Mucosa	Colon
10	chr15:40843200-40856400	Weak transcription	Fetal Heart	heart
11	chr15:40843800-40856400	Weak transcription	HSMMtube	muscle
12	chr15:40846000-40855600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:40846200-40856200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr15:40846600-40855800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:40846600-40856400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:40846600-40856400	Weak transcription	Right Atrium	heart
17	chr15:40846600-40856600	Weak transcription	Aorta	Aorta
18	chr15:40846600-40856600	Weak transcription	Gastric	stomach
19	chr15:40846800-40856000	Weak transcription	Stomach Mucosa	stomach
20	chr15:40847200-40855600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:40847200-40856400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr15:40847400-40856200	Weak transcription	Brain Germinal Matrix	brain
23	chr15:40847400-40856400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr15:40847400-40856600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr15:40848000-40856400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr15:40848000-40856400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr15:40848000-40856400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:40848000-40856400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:40848400-40856400	Weak transcription	NHDF-Ad	bronchial
30	chr15:40848600-40855800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr15:40848600-40856000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:40848600-40856200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr15:40848600-40856200	Weak transcription	HSMM	muscle
34	chr15:40848600-40856200	Weak transcription	HUVEC	blood vessel
35	chr15:40848600-40856200	Weak transcription	NHLF	lung
36	chr15:40848600-40856400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:40848600-40856400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr15:40848600-40856400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr15:40848600-40856400	Weak transcription	Brain Substantia Nigra	brain
40	chr15:40848600-40856400	Weak transcription	NH-A	brain
41	chr15:40848800-40855600	Weak transcription	HepG2	liver
42	chr15:40848800-40856200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr15:40848800-40856400	Weak transcription	Brain Angular Gyrus	brain
44	chr15:40848800-40856600	Weak transcription	Lung	lung
45	chr15:40849000-40856400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr15:40849000-40856600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr15:40849400-40856400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr15:40849600-40855800	Weak transcription	Primary T cells from cord blood	blood
49	chr15:40849600-40856200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr15:40849600-40856200	Weak transcription	Rectal Smooth Muscle	rectum

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