Variant report

Variant	rs12535024
Chromosome Location	chr7:50600178-50600179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IKZF1-1	chr7:50599969-50600290	NONHSAT120562

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1007702	1.00[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1007749	0.88[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575280	1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs11575332	1.00[EUR][1000 genomes]
rs11575359	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575400	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575413	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575424	1.00[AMR][1000 genomes]
rs11575425	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575506	1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12531158	0.81[AMR][1000 genomes]
rs1451370	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17665398	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17665588	1.00[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17665670	0.88[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1817073	0.88[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1868886	0.81[AMR][1000 genomes]
rs3735276	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3779075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3779076	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4947511	0.81[AMR][1000 genomes]
rs4947576	0.88[JPT][hapmap];1.00[AMR][1000 genomes]
rs4947580	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4947594	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4947634	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4948010	0.81[AMR][1000 genomes]
rs4948197	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4948201	0.88[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4948216	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6592962	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6951323	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6952938	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6953661	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6958793	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6959596	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6976009	0.81[AMR][1000 genomes]
rs731689	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7792474	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7800887	0.81[AMR][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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv888021	chr7:50538589-50610071	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50565200-50609000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr7:50595200-50604600	Genic enhancers	Fetal Intestine Small	intestine
3	chr7:50597000-50601200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:50597000-50601400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:50597200-50603600	Weak transcription	Liver	Liver
6	chr7:50597400-50601400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr7:50597800-50601400	Weak transcription	HepG2	liver
8	chr7:50597800-50602400	Weak transcription	Stomach Mucosa	stomach
9	chr7:50598200-50600400	Enhancers	HMEC	breast
10	chr7:50598400-50600200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:50598600-50600200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:50598800-50600200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:50598800-50600200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:50599000-50600200	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr7:50599000-50600200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr7:50599000-50600200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr7:50599000-50600200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:50599000-50600200	Enhancers	Brain Angular Gyrus	brain
19	chr7:50599000-50600200	Enhancers	NH-A	brain
20	chr7:50599400-50600200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:50599400-50600200	Genic enhancers	Fetal Intestine Large	intestine
22	chr7:50599600-50600200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr7:50599600-50600200	Enhancers	Brain Cingulate Gyrus	brain
24	chr7:50599600-50600200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
25	chr7:50599600-50600400	Enhancers	A549	lung
26	chr7:50599600-50601200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr7:50599600-50601400	Weak transcription	K562	blood
28	chr7:50599600-50601600	Weak transcription	NHLF	lung
29	chr7:50599600-50602600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr7:50599800-50600200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:50599800-50600200	Enhancers	Small Intestine	intestine
32	chr7:50599800-50600400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr7:50599800-50600400	Enhancers	NHEK	skin
34	chr7:50599800-50601400	Weak transcription	Hela-S3	cervix
35	chr7:50599800-50602400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr7:50599800-50602400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:50599800-50602400	Weak transcription	HUVEC	blood vessel
38	chr7:50599800-50602400	Weak transcription	NHDF-Ad	bronchial
39	chr7:50600000-50600200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:50600000-50600400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr7:50600000-50600600	Enhancers	Brain Germinal Matrix	brain
42	chr7:50600000-50601400	Weak transcription	Placenta	Placenta
43	chr7:50600000-50601400	Weak transcription	Pancreas	Pancrea
44	chr7:50600000-50601600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr7:50600000-50602200	Weak transcription	HSMM	muscle
46	chr7:50600000-50602400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr7:50600000-50602400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:50600000-50602400	Weak transcription	Brain Anterior Caudate	brain
49	chr7:50600000-50602400	Weak transcription	Osteobl	bone

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