Variant report

Variant	rs12125672
Chromosome Location	chr1:150554470-150554471
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
2	chr1:150548752..150555486-chr1:150599368..150605834,15	MCF-7	breast:
3	chr1:150550164..150555275-chr1:150782862..150788394,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143420	Chromatin interaction
ENSG00000200175	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1053732	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10888384	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10888385	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204668	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204669	0.93[ASN][1000 genomes]
rs11204675	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204676	0.81[AFR][1000 genomes]
rs11204677	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204678	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204679	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204680	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204684	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11585169	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12116492	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12126271	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12139563	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12406712	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12746899	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1971378	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2048558	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3738484	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738485	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754209	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4970918	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970923	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971041	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55862611	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61820165	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669122	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6697620	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6698495	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs878471	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs932054	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9803935	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
3	nsv535156	chr1:150540117-150575941	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv535157	chr1:150552692-150575941	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12125672	GOLPH3L	cis	Nerve Tibial	GTEx
rs12125672	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs12125672	CTSS	cis	Nerve Tibial	GTEx
rs12125672	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs12125672	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs12125672	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs12125672	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs12125672	HORMAD1	cis	Nerve Tibial	GTEx
rs12125672	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs12125672	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs12125672	ARNT	cis	Thyroid	GTEx
rs12125672	HORMAD1	cis	Esophagus Mucosa	GTEx
rs12125672	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150553000-150554800	Weak transcription	Primary T cells from cord blood	blood
2	chr1:150553000-150555000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:150553000-150555400	Enhancers	Primary B cells from peripheral blood	blood
4	chr1:150553000-150555600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:150553000-150556000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:150553000-150557000	Weak transcription	Fetal Stomach	stomach
7	chr1:150553000-150557200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:150553000-150559200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:150553000-150560600	Weak transcription	Right Atrium	heart
10	chr1:150553000-150562600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:150553000-150572800	Weak transcription	Thymus	Thymus
12	chr1:150553000-150583200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:150553200-150554600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:150553200-150554600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:150553200-150554800	Weak transcription	Primary B cells from cord blood	blood
16	chr1:150553200-150554800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:150553200-150554800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:150553200-150554800	Weak transcription	Osteobl	bone
19	chr1:150553200-150555000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:150553200-150555000	Weak transcription	HepG2	liver
21	chr1:150553200-150555200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:150553200-150555400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:150553200-150555400	Weak transcription	Placenta	Placenta
24	chr1:150553200-150558200	Weak transcription	Right Ventricle	heart
25	chr1:150553200-150564200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:150553200-150566000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:150553200-150568400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:150553200-150569400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:150553200-150569400	Weak transcription	Fetal Thymus	thymus
30	chr1:150553200-150572600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:150553200-150572600	Weak transcription	Fetal Brain Female	brain
32	chr1:150553200-150572800	Weak transcription	Brain Angular Gyrus	brain
33	chr1:150553200-150577600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:150553200-150581800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:150553200-150581800	Weak transcription	Dnd41	blood
36	chr1:150553200-150583200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:150553200-150592000	Weak transcription	Fetal Kidney	kidney
38	chr1:150553400-150554800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:150553400-150556400	Weak transcription	Fetal Intestine Small	intestine
40	chr1:150553800-150554800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:150553800-150554800	Enhancers	Pancreas	Pancrea
42	chr1:150553800-150568000	Weak transcription	HSMM	muscle
43	chr1:150553800-150572600	Weak transcription	Lung	lung
44	chr1:150553800-150576800	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:150554000-150555000	Weak transcription	HSMMtube	muscle
46	chr1:150554000-150555400	Weak transcription	Colonic Mucosa	Colon
47	chr1:150554000-150558400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:150554000-150560400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:150554000-150568400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:150554000-150568600	Weak transcription	Hela-S3	cervix

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