Variant report

Variant	rs1599750
Chromosome Location	chr12:58242545-58242546
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58175629..58177696-chr12:58241089..58243038,2	MCF-7	breast:
2	chr12:58240989..58243602-chr12:58264748..58266255,2	MCF-7	breast:
3	chr12:58242304..58245616-chr12:58249700..58252095,4	MCF-7	breast:
4	chr12:58233944..58243826-chr12:58273095..58290464,46	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123297	Chromatin interaction
ENSG00000245651	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10444569	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10747784	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10747786	0.87[CHD][hapmap];0.86[GIH][hapmap];0.86[AMR][1000 genomes]
rs10747787	0.87[CHD][hapmap];0.86[GIH][hapmap];0.86[AMR][1000 genomes]
rs10783850	0.88[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10783851	0.88[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783854	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783855	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783856	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877022	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10877024	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10877025	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10877026	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10877028	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap]
rs10877029	0.88[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10877030	0.88[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10877031	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10877032	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11172361	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172362	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172367	0.83[CHD][hapmap];0.86[GIH][hapmap];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11172368	0.85[AMR][1000 genomes]
rs11172369	0.84[AMR][1000 genomes]
rs11172371	0.82[AMR][1000 genomes]
rs12312955	0.85[AMR][1000 genomes]
rs12319233	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12426201	0.89[AMR][1000 genomes]
rs1599751	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1599931	0.88[JPT][hapmap];0.87[AMR][1000 genomes]
rs1875125	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1962047	0.80[CHD][hapmap]
rs2002275	0.80[CHD][hapmap];0.83[AMR][1000 genomes]
rs4237844	0.84[CHD][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4237845	0.80[CHD][hapmap]
rs4760171	0.87[ASW][hapmap];0.88[CEU][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4760172	0.88[CEU][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4760332	0.88[CEU][hapmap];0.90[CHD][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4760333	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4760335	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760339	0.83[CEU][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4760340	0.84[CHD][hapmap]
rs4760341	0.85[AMR][1000 genomes]
rs5017863	0.87[AMR][1000 genomes]
rs59401446	0.87[AMR][1000 genomes]
rs7134797	0.82[AMR][1000 genomes]
rs7298479	0.85[EUR][1000 genomes]
rs7312623	0.87[CHD][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes]
rs7489290	0.86[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7954957	0.80[CHD][hapmap]
rs7969844	0.83[AMR][1000 genomes]
rs870392	0.88[CEU][hapmap];0.90[CHD][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs871871	0.88[CEU][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9645819	0.86[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs1599750	METTL21B	cis	Muscle Skeletal	GTEx
rs1599750	FAM119B	cis	Temporal Cortex	GTEx
rs1599750	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs1599750	XRCC6BP1	cis	Whole Blood	GTEx
rs1599750	XRCC6BP1	cis	Artery Tibial	GTEx
rs1599750	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs1599750	FAM119B	cis	Frontal Cortex	GTEx
rs1599750	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs1599750	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs1599750	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs1599750	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs1599750	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs1599750	METTL21B	cis	lung	GTEx
rs1599750	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs1599750	FAM119B	cis	Cerebellum	GTEx
rs1599750	FAM119B	cis	lymphoblastoid	seeQTL
rs1599750	TSFM	cis	lymphoblastoid	seeQTL
rs1599750	METTL21B	cis	Esophagus Muscularis	GTEx
rs1599750	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs1599750	XRCC6BP1	cis	lung	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58241000-58242600	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr12:58241000-58244400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:58241200-58242600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:58241200-58242600	Enhancers	Adipose Nuclei	Adipose
5	chr12:58241200-58243400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:58241200-58244000	Weak transcription	Right Atrium	heart
7	chr12:58241200-58244200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:58241200-58244400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:58241200-58244400	Weak transcription	Aorta	Aorta
10	chr12:58241200-58244400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr12:58241200-58244400	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:58241200-58244400	Weak transcription	Left Ventricle	heart
13	chr12:58241200-58244400	Weak transcription	Right Ventricle	heart
14	chr12:58241200-58244600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:58241200-58244800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:58241200-58244800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:58241200-58244800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:58241200-58245000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:58241200-58245000	Weak transcription	Fetal Lung	lung
20	chr12:58241200-58245000	Weak transcription	A549	lung
21	chr12:58241200-58245600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:58241200-58245600	Weak transcription	NHDF-Ad	bronchial
23	chr12:58241200-58245800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:58241200-58245800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:58241200-58246000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:58241200-58246000	Weak transcription	Fetal Brain Male	brain
27	chr12:58241200-58246000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr12:58241200-58246000	Weak transcription	HMEC	breast
29	chr12:58241200-58246200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:58241400-58242800	Enhancers	Thymus	Thymus
31	chr12:58241400-58243200	Enhancers	K562	blood
32	chr12:58241400-58244400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:58241400-58244400	Weak transcription	Brain Substantia Nigra	brain
34	chr12:58241400-58244400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr12:58241400-58244400	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr12:58241400-58244800	Weak transcription	Brain Germinal Matrix	brain
37	chr12:58241400-58244800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:58241400-58245800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:58241600-58243600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:58241800-58242800	Enhancers	Brain Anterior Caudate	brain
41	chr12:58241800-58244000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr12:58241800-58244000	Weak transcription	Spleen	Spleen
43	chr12:58241800-58244200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr12:58241800-58244200	Weak transcription	Placenta	Placenta
45	chr12:58241800-58244200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr12:58241800-58244400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:58241800-58244800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:58241800-58245000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr12:58241800-58245200	Weak transcription	Colonic Mucosa	Colon
50	chr12:58242000-58242600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links