Variant report

Variant	rs12030596
Chromosome Location	chr1:155536437-155536438
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	POLR2A	chr1:155535777-155536485	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155530671..155532502-chr1:155535326..155537191,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271267	TF binding region
ASH1L	TF binding region
ENSG00000235919	Chromatin interaction
ENSG00000116539	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10752611	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10796943	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10796945	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10796946	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10796947	0.95[ASN][1000 genomes]
rs10908465	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10908466	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908467	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908469	0.83[EUR][1000 genomes]
rs10908470	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908471	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908472	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908479	0.86[EUR][1000 genomes]
rs11264371	0.88[ASN][1000 genomes]
rs11264372	0.88[ASN][1000 genomes]
rs11264374	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11264375	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11264380	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264381	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264383	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264386	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264387	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264393	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11264397	0.89[EUR][1000 genomes]
rs11264398	0.89[EUR][1000 genomes]
rs11582072	0.95[ASN][1000 genomes]
rs12022088	0.89[EUR][1000 genomes]
rs12026638	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12028416	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12037824	0.86[ASN][1000 genomes]
rs12039893	0.89[EUR][1000 genomes]
rs12040100	0.89[EUR][1000 genomes]
rs12041534	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12046473	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12047626	0.84[EUR][1000 genomes]
rs12047756	0.88[EUR][1000 genomes]
rs12048286	0.83[AMR][1000 genomes]
rs12067371	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12079134	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12091730	0.84[AMR][1000 genomes]
rs12093350	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12239100	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12724079	0.89[ASN][1000 genomes]
rs12740629	0.84[EUR][1000 genomes]
rs12746592	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758945	0.83[EUR][1000 genomes]
rs1325908	0.86[ASN][1000 genomes]
rs1360554	0.94[ASN][1000 genomes]
rs2048431	0.88[EUR][1000 genomes]
rs2175391	0.88[EUR][1000 genomes]
rs34124416	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34620961	0.85[EUR][1000 genomes]
rs348186	0.84[EUR][1000 genomes]
rs35615695	0.97[ASN][1000 genomes]
rs3738590	0.86[EUR][1000 genomes]
rs3851912	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3892792	0.93[EUR][1000 genomes]
rs475550	0.86[EUR][1000 genomes]
rs4971095	0.89[EUR][1000 genomes]
rs6427278	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6672128	0.86[EUR][1000 genomes]
rs6684889	0.89[ASN][1000 genomes]
rs6688636	0.95[ASN][1000 genomes]
rs6696888	0.99[ASN][1000 genomes]
rs7411786	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7521594	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv1795662	chr1:155305059-155540660	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS 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 miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv872468	chr1:155413304-155549562	Active TSS Weak transcription Strong transcription Flanking 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	33 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12030596	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs12030596	GBAP1	cis	Artery Tibial	GTEx
rs12030596	GBA	cis	Esophagus Mucosa	GTEx
rs12030596	FDPS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155533400-155549000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:155534000-155539400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:155534200-155542800	Weak transcription	Esophagus	oesophagus
4	chr1:155534200-155543000	Weak transcription	Brain Germinal Matrix	brain
5	chr1:155534200-155547600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:155534400-155540000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:155534400-155544200	Weak transcription	Fetal Brain Female	brain
8	chr1:155534600-155536800	Weak transcription	Fetal Kidney	kidney
9	chr1:155534600-155537800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:155534600-155539200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:155534600-155539800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:155534600-155539800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:155534600-155539800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:155534600-155539800	Weak transcription	Fetal Heart	heart
15	chr1:155534600-155539800	Weak transcription	NH-A	brain
16	chr1:155534600-155540000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:155534600-155540000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:155534600-155540000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:155534600-155540200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:155534600-155542000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:155534600-155542000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:155534600-155542000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:155534600-155542200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:155534600-155542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:155534600-155542400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:155534600-155542400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:155534600-155543000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:155534600-155543000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:155534600-155560400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:155534600-155565800	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:155534800-155536800	Weak transcription	Fetal Brain Male	brain
32	chr1:155534800-155537000	Weak transcription	Adipose Nuclei	Adipose
33	chr1:155534800-155539400	Weak transcription	Primary T cells from cord blood	blood
34	chr1:155534800-155539800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:155534800-155539800	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr1:155534800-155540000	Weak transcription	Spleen	Spleen
37	chr1:155534800-155540200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr1:155534800-155540200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:155534800-155540200	Weak transcription	Left Ventricle	heart
40	chr1:155534800-155540800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:155534800-155541000	Weak transcription	HSMMtube	muscle
42	chr1:155534800-155542200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:155534800-155542600	Weak transcription	NHLF	lung
44	chr1:155534800-155543000	Weak transcription	HepG2	liver
45	chr1:155534800-155543200	Weak transcription	Pancreas	Pancrea
46	chr1:155534800-155544800	Weak transcription	Brain Anterior Caudate	brain
47	chr1:155534800-155558200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:155534800-155561800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:155534800-155565600	Weak transcription	Brain Angular Gyrus	brain
50	chr1:155534800-155568400	Weak transcription	Thymus	Thymus

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