Variant report

Variant	rs2025669
Chromosome Location	chr1:155357609-155357610
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	chr1:155349409..155351647-chr1:155355555..155357785,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10752611	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10796943	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10796944	0.82[AMR][1000 genomes]
rs10796945	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10796946	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10908465	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10908466	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10908467	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10908469	0.83[EUR][1000 genomes]
rs10908470	0.82[AMR][1000 genomes]
rs11264362	0.85[ASN][1000 genomes]
rs11264363	0.86[ASN][1000 genomes]
rs11264366	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11264367	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11264369	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264370	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264371	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11264372	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11264374	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11264375	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11264380	0.82[EUR][1000 genomes]
rs11264381	0.81[AMR][1000 genomes]
rs12021631	0.87[ASN][1000 genomes]
rs12024696	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12025532	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12026638	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12028416	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12037824	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12041534	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12046473	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12049455	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12067371	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12079134	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12081067	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131079	0.88[ASN][1000 genomes]
rs12239100	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12239114	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12746592	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5005770	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56675301	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6670014	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs66923802	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71517782	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7411786	0.82[EUR][1000 genomes]
rs7416976	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556102	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv872467	chr1:155345641-155377171	Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2025669	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs2025669	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs2025669	GBAP1	cis	Artery Tibial	GTEx
rs2025669	GBA	cis	Esophagus Mucosa	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155306200-155375400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:155312400-155407400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:155330200-155362400	Weak transcription	Stomach Mucosa	stomach
4	chr1:155340600-155361200	Weak transcription	Fetal Heart	heart
5	chr1:155340600-155362600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:155340600-155364200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:155340800-155361800	Weak transcription	Right Ventricle	heart
8	chr1:155340800-155364800	Weak transcription	Small Intestine	intestine
9	chr1:155345600-155403000	Weak transcription	Esophagus	oesophagus
10	chr1:155346000-155358000	Weak transcription	Pancreas	Pancrea
11	chr1:155346400-155357800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:155347400-155361000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:155347400-155364000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:155347400-155407400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:155347600-155358000	Weak transcription	Lung	lung
16	chr1:155347600-155368400	Weak transcription	Colonic Mucosa	Colon
17	chr1:155347600-155376000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:155348200-155358000	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:155348200-155360800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:155348200-155362800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:155348200-155373800	Weak transcription	Spleen	Spleen
22	chr1:155348200-155380800	Weak transcription	HMEC	breast
23	chr1:155348200-155386000	Weak transcription	NHEK	skin
24	chr1:155348600-155363600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:155348800-155361800	Weak transcription	Psoas Muscle	Psoas
26	chr1:155349400-155407600	Weak transcription	Aorta	Aorta
27	chr1:155349800-155362400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:155349800-155364600	Weak transcription	HepG2	liver
29	chr1:155349800-155390800	Weak transcription	Brain Anterior Caudate	brain
30	chr1:155349800-155403000	Weak transcription	NHLF	lung
31	chr1:155350000-155357800	Weak transcription	Ovary	ovary
32	chr1:155350000-155359400	Weak transcription	HUVEC	blood vessel
33	chr1:155350000-155362600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:155350000-155364000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:155350000-155399200	Weak transcription	Brain Angular Gyrus	brain
36	chr1:155350000-155402400	Weak transcription	Brain Substantia Nigra	brain
37	chr1:155350200-155399200	Weak transcription	NH-A	brain
38	chr1:155351000-155361800	Weak transcription	Left Ventricle	heart
39	chr1:155352400-155359000	Strong transcription	Fetal Intestine Large	intestine
40	chr1:155352800-155357800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:155352800-155364000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:155353600-155359800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:155354400-155359600	Strong transcription	Thymus	Thymus
44	chr1:155354400-155366200	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:155354600-155357800	Weak transcription	HSMM	muscle
46	chr1:155354600-155358400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:155355000-155367000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:155355200-155365800	Strong transcription	Liver	Liver
49	chr1:155355400-155358400	Strong transcription	Duodenum Mucosa	Duodenum
50	chr1:155355400-155358400	Strong transcription	Osteobl	bone

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