Variant report

Variant	rs13249364
Chromosome Location	chr8:86085707-86085708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:85971850..85974054-chr8:86083102..86085878,2	MCF-7	breast:
2	chr8:86085188..86087448-chr8:86092785..86094662,2	K562	blood:
3	chr8:86081116..86086667-chr8:86087249..86091759,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254208	Chromatin interaction
ENSG00000260493	Chromatin interaction
ENSG00000133740	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10088120	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10091577	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10091710	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10100442	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12549421	0.87[ASN][1000 genomes]
rs12926	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13269031	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13269739	0.90[ASN][1000 genomes]
rs16913681	0.82[AMR][1000 genomes]
rs2403082	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2403083	0.82[ASN][1000 genomes]
rs2403084	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2403085	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2403086	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2403088	0.92[EUR][1000 genomes]
rs2403089	0.83[EUR][1000 genomes]
rs28621707	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2896454	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34103685	0.92[ASN][1000 genomes]
rs34527380	0.92[ASN][1000 genomes]
rs3779899	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4150859	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4150862	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150865	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4150867	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4150868	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4150869	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4150884	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4150893	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4150897	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4150942	0.85[EUR][1000 genomes]
rs4740043	0.92[EUR][1000 genomes]
rs62527168	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62527173	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6605609	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6605624	0.81[EUR][1000 genomes]
rs6605625	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6986704	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7004765	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7008032	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7010228	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7015758	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7814435	0.81[AMR][1000 genomes]
rs7818090	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7823218	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7829050	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7842013	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3481417	chr8:85279453-86145229	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3481418	chr8:85279453-86145229	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1799571	chr8:86064130-86105803	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13249364	LRRCC1	cis	Esophagus Mucosa	GTEx
rs13249364	LRRCC1	cis	Artery Tibial	GTEx
rs13249364	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs13249364	C8orf59	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86083600-86088600	Enhancers	Primary B cells from cord blood	blood
2	chr8:86084000-86088800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:86084600-86086800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr8:86084600-86087400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr8:86084600-86088600	Weak transcription	Thymus	Thymus
6	chr8:86084600-86088600	Weak transcription	K562	blood
7	chr8:86084600-86088800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr8:86084600-86088800	Weak transcription	Primary T cells from cord blood	blood
9	chr8:86084800-86087200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr8:86084800-86087400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr8:86084800-86088600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr8:86084800-86088600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr8:86084800-86088600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr8:86084800-86088800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr8:86084800-86088800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr8:86085200-86088800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr8:86085400-86086200	Weak transcription	Fetal Thymus	thymus
18	chr8:86085400-86087400	Weak transcription	GM12878-XiMat	blood
19	chr8:86085400-86088800	Weak transcription	Liver	Liver
20	chr8:86085600-86088800	Weak transcription	HepG2	liver

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