Variant report

Variant	rs6427278
Chromosome Location	chr1:155562583-155562584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155290471..155293068-chr1:155560702..155562665,2	MCF-7	breast:
2	chr1:155561838..155563770-chr1:155565772..155568084,2	K562	blood:

Variant related genes	Relation type
ENSG00000225855	Chromatin interaction
ENSG00000160753	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10752611	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10796947	0.81[ASN][1000 genomes]
rs10908470	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10908471	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10908472	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10908479	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11264380	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11264381	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11264383	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11264386	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264387	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264393	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11264397	0.92[EUR][1000 genomes]
rs11264398	0.92[EUR][1000 genomes]
rs11582072	0.81[ASN][1000 genomes]
rs12022088	0.92[EUR][1000 genomes]
rs12030596	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12039893	0.92[EUR][1000 genomes]
rs12040100	0.92[EUR][1000 genomes]
rs12047626	0.88[EUR][1000 genomes]
rs12047756	0.91[EUR][1000 genomes]
rs12091730	0.81[EUR][1000 genomes]
rs12093350	0.88[EUR][1000 genomes]
rs12740629	0.88[EUR][1000 genomes]
rs12746592	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12758945	0.86[EUR][1000 genomes]
rs1360554	0.80[ASN][1000 genomes]
rs2048431	0.91[EUR][1000 genomes]
rs2175391	0.91[EUR][1000 genomes]
rs34124416	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34620961	0.88[EUR][1000 genomes]
rs348186	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35615695	0.83[ASN][1000 genomes]
rs3738590	0.89[EUR][1000 genomes]
rs3851912	0.94[EUR][1000 genomes]
rs3892792	0.95[EUR][1000 genomes]
rs4550031	0.83[EUR][1000 genomes]
rs475550	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4971095	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6672128	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6688636	0.81[ASN][1000 genomes]
rs6696888	0.85[ASN][1000 genomes]
rs7411786	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7521594	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	esv3431739	chr1:155514331-155664183	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	esv3388968	chr1:155532335-155658278	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv1002390	chr1:155553423-155706930	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv436522	chr1:155559513-155674249	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription 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	40 gene(s)	inside rSNPs	diseases
8	nsv946419	chr1:155561148-155630744	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	esv3360339	chr1:155562157-155683127	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6427278	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs6427278	GBAP1	cis	Artery Tibial	GTEx
rs6427278	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs6427278	GBA	cis	Esophagus Mucosa	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155534600-155565800	Weak transcription	Brain Hippocampus Middle	brain
2	chr1:155534800-155565600	Weak transcription	Brain Angular Gyrus	brain
3	chr1:155534800-155568400	Weak transcription	Thymus	Thymus
4	chr1:155535000-155570400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:155535400-155564000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:155540400-155565800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:155541400-155569000	Weak transcription	HSMMtube	muscle
8	chr1:155541600-155565600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:155541600-155565600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:155541600-155568400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:155542000-155565600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:155542200-155562800	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:155554000-155566400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:155557200-155568600	Weak transcription	NHEK	skin
15	chr1:155558400-155568600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:155559000-155568800	Weak transcription	HSMM	muscle
17	chr1:155559200-155565600	Weak transcription	Fetal Brain Female	brain
18	chr1:155560600-155565800	Weak transcription	Brain Anterior Caudate	brain
19	chr1:155560600-155568400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:155560600-155568400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:155560600-155570400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:155561000-155568800	Weak transcription	Lung	lung
23	chr1:155561200-155568400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:155561200-155568600	Weak transcription	Fetal Stomach	stomach
25	chr1:155561400-155568200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:155562000-155564200	Weak transcription	Brain Germinal Matrix	brain
27	chr1:155562200-155565600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:155562200-155570200	Weak transcription	Hela-S3	cervix

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