Variant report

Variant	rs12023976
Chromosome Location	chr1:175952532-175952533
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10494495	0.84[EUR][1000 genomes]
rs10494498	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10753112	0.84[EUR][1000 genomes]
rs10798425	0.83[EUR][1000 genomes]
rs10798434	0.85[EUR][1000 genomes]
rs10913112	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10913116	0.84[EUR][1000 genomes]
rs10913117	0.85[EUR][1000 genomes]
rs10913120	0.82[EUR][1000 genomes]
rs10913128	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12030638	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12040241	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12047295	1.00[YRI][hapmap]
rs35846379	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3748618	1.00[YRI][hapmap]
rs4409605	0.84[EUR][1000 genomes]
rs6673760	1.00[YRI][hapmap]
rs6703511	0.83[EUR][1000 genomes]
rs7515914	0.85[EUR][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	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872561	chr1:175949646-176092167	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12023976	RP11-318C24.2	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175897000-175953000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:175897600-175953200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:175898600-175953200	Weak transcription	Pancreas	Pancrea
4	chr1:175899200-175953200	Weak transcription	Esophagus	oesophagus
5	chr1:175904200-175956200	Weak transcription	Psoas Muscle	Psoas
6	chr1:175904600-175953000	Weak transcription	Right Ventricle	heart
7	chr1:175906400-175962600	Weak transcription	NH-A	brain
8	chr1:175908000-175959400	Weak transcription	NHEK	skin
9	chr1:175917600-175953000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:175924600-175953200	Weak transcription	Gastric	stomach
11	chr1:175924600-175953200	Weak transcription	HepG2	liver
12	chr1:175940400-175953800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:175941000-175952600	Weak transcription	Colonic Mucosa	Colon
14	chr1:175941000-175953200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:175941200-175952800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:175941200-175953200	Weak transcription	Lung	lung
17	chr1:175945800-175953400	Weak transcription	Aorta	Aorta
18	chr1:175946000-175996000	Weak transcription	HMEC	breast
19	chr1:175947600-175952800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:175948200-175952800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:175948200-175957400	Weak transcription	Brain Substantia Nigra	brain
22	chr1:175948200-175961400	Weak transcription	NHLF	lung
23	chr1:175948400-175953400	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:175948600-175953400	Weak transcription	HUVEC	blood vessel
25	chr1:175949200-175953400	Strong transcription	Primary T cells from cord blood	blood
26	chr1:175949200-175958600	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:175949200-175958600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:175949400-175957000	Weak transcription	Osteobl	bone
29	chr1:175949600-175954800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:175949800-175954800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:175950000-175952600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:175950000-175952800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:175950000-175954000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:175950000-175954200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:175950000-175961200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:175950200-175952800	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:175950200-175953000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:175950200-175955400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:175950200-175956400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:175950400-175952600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:175950400-175954800	ZNF genes & repeats	Primary B cells from cord blood	blood
42	chr1:175950400-175955000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
43	chr1:175950400-175955000	ZNF genes & repeats	GM12878-XiMat	blood
44	chr1:175950600-175952600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:175950600-175953200	ZNF genes & repeats	Fetal Lung	lung
46	chr1:175950600-175953600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:175950600-175954800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
48	chr1:175950800-175952800	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:175950800-175953800	ZNF genes & repeats	Liver	Liver
50	chr1:175951000-175952800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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