Variant report

Variant	rs11832727
Chromosome Location	chr12:49999275-49999276
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	chr12:49993213..49995668-chr12:49998189..50000775,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNH3-1	chr12:49997960-50001023	ENSG00000250952
2	lnc-FAM186B-2	chr12:49998985-49999410	NR_027450

Variant related genes	Relation type
ENSG00000135436	Chromatin interaction
ENSG00000110844	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11830472	1.00[GIH][hapmap];1.00[YRI][hapmap]
rs11831673	1.00[YRI][hapmap]
rs11831877	0.94[AFR][1000 genomes]
rs11832420	1.00[YRI][hapmap]
rs11835085	1.00[YRI][hapmap]
rs11837399	1.00[AFR][1000 genomes]
rs11837408	1.00[AFR][1000 genomes]
rs11837637	1.00[ASW][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs3861577	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs57489906	0.81[AFR][1000 genomes]
rs58072420	0.94[AFR][1000 genomes]
rs59576871	0.91[AFR][1000 genomes]
rs59597892	1.00[AFR][1000 genomes]
rs59957222	0.86[AFR][1000 genomes]
rs60117004	0.94[AFR][1000 genomes]
rs7131756	0.94[AFR][1000 genomes]
rs7134329	1.00[AFR][1000 genomes]
rs7307183	1.00[AFR][1000 genomes]
rs7310069	0.81[AFR][1000 genomes]
rs7312037	0.94[AFR][1000 genomes]
rs7313183	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs7313590	0.94[AFR][1000 genomes]
rs7960185	1.00[YRI][hapmap]
rs7978381	1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap]

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	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
4	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49963000-50003200	Weak transcription	Aorta	Aorta
2	chr12:49979600-50002600	Weak transcription	HepG2	liver
3	chr12:49980400-50000200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:49982600-50015400	Weak transcription	Pancreas	Pancrea
5	chr12:49983200-49999400	Weak transcription	HSMMtube	muscle
6	chr12:49983200-50002800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr12:49983400-50002800	Weak transcription	NHEK	skin
8	chr12:49985200-50003000	Weak transcription	Lung	lung
9	chr12:49992800-50003200	Weak transcription	Fetal Intestine Large	intestine
10	chr12:49994000-50002600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:49994400-50002800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:49994400-50003200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:49994400-50004400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:49994600-50000200	Weak transcription	Adipose Nuclei	Adipose
15	chr12:49994600-50003200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:49994600-50005800	Weak transcription	Liver	Liver
17	chr12:49994800-50000800	Weak transcription	Fetal Brain Female	brain
18	chr12:49995000-50002600	Weak transcription	Fetal Intestine Small	intestine
19	chr12:49995000-50003000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:49995200-50002800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:49995400-50002800	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:49996800-50005400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:49998000-49999400	Enhancers	Fetal Stomach	stomach
24	chr12:49998000-50000800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr12:49998400-49999400	Enhancers	Fetal Heart	heart
26	chr12:49998600-49999400	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr12:49998600-49999400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:49998600-49999400	Enhancers	Placenta	Placenta
29	chr12:49998800-49999400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:49998800-49999400	Enhancers	Fetal Thymus	thymus
31	chr12:49999000-49999400	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr12:49999000-49999400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr12:49999000-49999400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr12:49999000-49999400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr12:49999000-49999400	Enhancers	Dnd41	blood
36	chr12:49999200-49999400	Enhancers	Ovary	ovary
37	chr12:49999200-49999400	Enhancers	Right Ventricle	heart
38	chr12:49999200-50002800	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links