Variant report

Variant	rs12047860
Chromosome Location	chr1:247501489-247501490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247500532..247503648-chr1:247521272..247523608,4	K562	blood:
2	chr1:247484997..247486937-chr1:247500462..247503140,2	K562	blood:
3	chr1:247497896..247501644-chr1:247501987..247504336,4	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10754545	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1192833	0.81[ASN][1000 genomes]
rs12023326	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12023478	0.81[ASN][1000 genomes]
rs12026978	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12027522	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12034916	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12034919	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12035371	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12035515	0.85[AMR][1000 genomes]
rs12048553	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12404914	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17664745	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3850825	0.82[ASN][1000 genomes]
rs56013900	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56322048	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56335231	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56366903	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56396334	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56740645	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6426239	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6690864	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6697861	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7522071	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
3	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a
5	nsv873439	chr1:247486736-247549220	Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12047860	ZNF496	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247496200-247503000	Weak transcription	Aorta	Aorta
2	chr1:247496400-247501600	Enhancers	Primary hematopoietic stem cells	blood
3	chr1:247496400-247511000	Weak transcription	Primary B cells from cord blood	blood
4	chr1:247496600-247505800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:247496600-247506000	Weak transcription	HSMMtube	muscle
6	chr1:247496600-247511000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:247496800-247502000	Weak transcription	HSMM	muscle
8	chr1:247496800-247502200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:247496800-247503000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:247496800-247507200	Weak transcription	Fetal Intestine Large	intestine
11	chr1:247496800-247510200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:247497000-247501600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:247497000-247503000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:247497000-247504000	Weak transcription	Stomach Mucosa	stomach
15	chr1:247497000-247511200	Weak transcription	Esophagus	oesophagus
16	chr1:247497200-247502200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:247497200-247503000	Weak transcription	NHEK	skin
18	chr1:247497200-247505800	Weak transcription	Brain Substantia Nigra	brain
19	chr1:247497200-247506200	Weak transcription	HMEC	breast
20	chr1:247497200-247509800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:247497200-247516000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:247497400-247503000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:247497400-247511200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:247497400-247511400	Weak transcription	Primary T cells from cord blood	blood
25	chr1:247497800-247502800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:247497800-247506400	Weak transcription	GM12878-XiMat	blood
27	chr1:247498000-247502800	Weak transcription	Hela-S3	cervix
28	chr1:247498200-247501800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr1:247498200-247501800	Weak transcription	Psoas Muscle	Psoas
30	chr1:247498400-247501600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:247498400-247502000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:247498400-247503000	Weak transcription	A549	lung
33	chr1:247498400-247503200	Weak transcription	Fetal Intestine Small	intestine
34	chr1:247498800-247502600	Weak transcription	Dnd41	blood
35	chr1:247498800-247505200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:247499000-247501600	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr1:247499200-247501600	Genic enhancers	Fetal Thymus	thymus
38	chr1:247499200-247502800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr1:247499200-247503000	Weak transcription	Spleen	Spleen
40	chr1:247499400-247503000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:247499600-247506200	Weak transcription	HUVEC	blood vessel
42	chr1:247499600-247511000	Weak transcription	Adipose Nuclei	Adipose
43	chr1:247499600-247511200	Weak transcription	Brain Germinal Matrix	brain
44	chr1:247499800-247503000	Weak transcription	Lung	lung
45	chr1:247499800-247506200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:247499800-247510800	Weak transcription	Right Atrium	heart
47	chr1:247500000-247502200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:247500000-247502600	Enhancers	Osteobl	bone
49	chr1:247500000-247503000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:247500000-247503000	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links