Variant report

Variant	rs12239100
Chromosome Location	chr1:155428476-155428477
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155428176..155430935-chr1:155448192..155450755,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10752611	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10796943	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10796944	0.90[AMR][1000 genomes]
rs10796945	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10796946	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10796947	0.93[ASN][1000 genomes]
rs10908465	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908466	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908467	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908469	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10908470	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10908471	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908472	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11264366	0.86[EUR][1000 genomes]
rs11264367	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11264369	0.83[EUR][1000 genomes]
rs11264370	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11264371	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264372	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264374	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264375	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264380	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11264381	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11264383	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11264386	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11264387	0.81[AMR][1000 genomes]
rs11582072	0.93[ASN][1000 genomes]
rs12024696	0.80[EUR][1000 genomes]
rs12025532	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12026638	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12028416	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12030596	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12037824	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12041534	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12046473	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12067371	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12079134	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12081067	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12239114	0.80[EUR][1000 genomes]
rs12724079	0.99[ASN][1000 genomes]
rs12746592	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1325908	0.96[ASN][1000 genomes]
rs1360554	0.92[ASN][1000 genomes]
rs2025669	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35615695	0.87[ASN][1000 genomes]
rs5005770	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56675301	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6684889	0.99[ASN][1000 genomes]
rs6688636	0.93[ASN][1000 genomes]
rs66923802	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6696888	0.89[ASN][1000 genomes]
rs71517782	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7411786	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7416976	0.90[AMR][1000 genomes];0.90[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	nsv831636	chr1:155219223-155444864	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	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
4	esv1799856	chr1:155305059-155534616	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking 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
5	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
6	esv1795478	chr1:155334933-155510824	Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1803551	chr1:155334933-155522572	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv1800974	chr1:155367680-155510824	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12239100	GBAP1	cis	Artery Tibial	GTEx
rs12239100	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs12239100	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs12239100	GBA	cis	Esophagus Mucosa	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155362200-155433400	Weak transcription	Psoas Muscle	Psoas
2	chr1:155362800-155442400	Weak transcription	Right Ventricle	heart
3	chr1:155364400-155450800	Weak transcription	HUVEC	blood vessel
4	chr1:155404600-155441400	Weak transcription	Esophagus	oesophagus
5	chr1:155408600-155444200	Weak transcription	Fetal Brain Male	brain
6	chr1:155408600-155448400	Weak transcription	Fetal Brain Female	brain
7	chr1:155408800-155435400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:155408800-155437000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:155408800-155441000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:155408800-155441000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:155408800-155441200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:155408800-155447600	Weak transcription	Aorta	Aorta
13	chr1:155409000-155434200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:155409400-155431800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:155412000-155429200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:155412200-155433800	Weak transcription	NHEK	skin
17	chr1:155412200-155436600	Weak transcription	HMEC	breast
18	chr1:155418600-155435400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:155419200-155434400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:155419400-155433800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:155419800-155429800	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:155420000-155430200	Strong transcription	Dnd41	blood
23	chr1:155420600-155432600	Weak transcription	Colonic Mucosa	Colon
24	chr1:155420600-155441000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:155420800-155429200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:155420800-155439400	Weak transcription	Fetal Kidney	kidney
27	chr1:155421000-155436600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:155421200-155429200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:155421600-155432000	Weak transcription	GM12878-XiMat	blood
30	chr1:155421600-155435600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:155421600-155441000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:155421600-155441600	Weak transcription	Brain Germinal Matrix	brain
33	chr1:155421800-155441200	Weak transcription	Ovary	ovary
34	chr1:155421800-155447800	Weak transcription	Lung	lung
35	chr1:155422800-155436400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr1:155423000-155429800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:155423000-155431600	Weak transcription	Left Ventricle	heart
38	chr1:155423000-155441200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:155423200-155431600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:155423200-155432000	Weak transcription	A549	lung
41	chr1:155423400-155441200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:155423800-155436400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:155424400-155431800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:155424400-155431800	Weak transcription	Fetal Intestine Large	intestine
45	chr1:155424400-155441000	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:155424600-155462600	Weak transcription	Pancreas	Pancrea
47	chr1:155425400-155429800	Strong transcription	Fetal Thymus	thymus
48	chr1:155425600-155428600	Enhancers	HepG2	liver
49	chr1:155425600-155429600	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:155425800-155428600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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