Variant report

Variant	rs1060293
Chromosome Location	chr15:42837498-42837499
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	EGR1	chr15:42837473-42837777	K562	blood:	n/a	n/a
2	MYC	chr15:42837346-42837546	K562	blood:	n/a	n/a
3	TEAD4	chr15:42837065-42837742	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42837304..42838910-chr15:42839465..42842272,2	MCF-7	breast:

Variant related genes	Relation type
HAUS2	TF binding region
ENSG00000137814	Chromatin interaction
ENSG00000180979	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10518766	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060291	1.00[ASN][1000 genomes]
rs11022	1.00[ASN][1000 genomes]
rs11070376	1.00[ASN][1000 genomes]
rs11636577	1.00[ASN][1000 genomes]
rs16973320	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17709180	1.00[ASN][1000 genomes]
rs17709377	1.00[ASN][1000 genomes]
rs17766532	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900921	1.00[ASN][1000 genomes]
rs2899051	1.00[ASN][1000 genomes]
rs2899059	0.83[EUR][1000 genomes]
rs34359922	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34643746	1.00[ASN][1000 genomes]
rs34792942	1.00[ASN][1000 genomes]
rs3986280	1.00[ASN][1000 genomes]
rs4923948	1.00[ASN][1000 genomes]
rs4924684	1.00[ASN][1000 genomes]
rs4924687	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56357092	1.00[ASN][1000 genomes]
rs56982416	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58042601	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58641431	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59697584	1.00[ASN][1000 genomes]
rs59705032	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60380503	1.00[ASN][1000 genomes]
rs60584955	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60812675	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61489160	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022317	1.00[ASN][1000 genomes]
rs7180483	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73402783	1.00[ASN][1000 genomes]
rs73402785	1.00[ASN][1000 genomes]
rs73404714	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73404717	0.80[EUR][1000 genomes]
rs73404723	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73404730	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73404763	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73406518	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73406534	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73406545	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74009095	1.00[ASN][1000 genomes]
rs8033412	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1060293	LRRC57	cis	Thyroid	GTEx
rs1060293	LRRC57	Cis_1M	lymphoblastoid	RTeQTL
rs1060293	LRRC57	cis	Esophagus Muscularis	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42797400-42839800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:42797600-42839400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:42799200-42839400	Weak transcription	Stomach Mucosa	stomach
4	chr15:42802400-42839200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:42803600-42839400	Weak transcription	A549	lung
6	chr15:42806200-42839000	Weak transcription	Fetal Brain Male	brain
7	chr15:42808400-42839000	Weak transcription	Fetal Heart	heart
8	chr15:42810200-42840200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:42811000-42837600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr15:42817400-42840200	Weak transcription	Pancreas	Pancrea
11	chr15:42821200-42839800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:42822200-42840200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:42822800-42840000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:42823400-42840200	Weak transcription	Psoas Muscle	Psoas
15	chr15:42823800-42838000	Weak transcription	Brain Angular Gyrus	brain
16	chr15:42824000-42840200	Weak transcription	Small Intestine	intestine
17	chr15:42824400-42839400	Weak transcription	Brain Substantia Nigra	brain
18	chr15:42824600-42838400	Weak transcription	HepG2	liver
19	chr15:42824600-42839600	Weak transcription	Right Ventricle	heart
20	chr15:42830600-42837600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr15:42831000-42837800	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:42831200-42839000	Strong transcription	Fetal Lung	lung
23	chr15:42831400-42839200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:42831600-42839000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:42831600-42840200	Weak transcription	Gastric	stomach
26	chr15:42833400-42838000	Strong transcription	Primary T cells from cord blood	blood
27	chr15:42833400-42838200	Strong transcription	Placenta	Placenta
28	chr15:42833400-42838400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr15:42833600-42837800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr15:42834000-42838000	Strong transcription	Fetal Intestine Large	intestine
31	chr15:42834200-42837600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:42834400-42837800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:42834400-42838000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr15:42834400-42838000	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr15:42834400-42839200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:42834400-42839400	Strong transcription	Fetal Muscle Leg	muscle
37	chr15:42834600-42837600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:42834600-42837800	Strong transcription	HUVEC	blood vessel
39	chr15:42834600-42838200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:42834600-42838400	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:42834600-42838400	Strong transcription	Liver	Liver
42	chr15:42834800-42837600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:42834800-42837600	Strong transcription	Adipose Nuclei	Adipose
44	chr15:42834800-42837600	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr15:42834800-42838200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr15:42834800-42838600	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr15:42834800-42838800	Strong transcription	Primary B cells from peripheral blood	blood
48	chr15:42835000-42838000	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:42835000-42838000	Strong transcription	NHEK	skin
50	chr15:42835000-42838200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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