Variant report

Variant	rs12024508
Chromosome Location	chr1:85914456-85914457
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85913232..85915386-chr1:85917552..85919124,2	K562	blood:
2	chr1:85911377..85913833-chr1:85913866..85915628,2	MCF-7	breast:
3	chr1:85912844..85915674-chr1:86040925..86042753,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153904	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12021849	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12022443	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12022538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023006	0.85[ASN][1000 genomes]
rs12023795	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12024405	0.85[ASN][1000 genomes]
rs12029474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12029684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12033170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12033315	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12033473	0.85[ASN][1000 genomes]
rs12034206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12034481	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12036146	0.85[ASN][1000 genomes]
rs12038279	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12039188	0.85[ASN][1000 genomes]
rs12041140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12042485	0.85[ASN][1000 genomes]
rs12043505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12043604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045545	0.85[ASN][1000 genomes]
rs12046433	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12047139	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12047220	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12048263	0.85[ASN][1000 genomes]
rs12049582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1851782	0.92[EUR][1000 genomes]
rs2300638	0.85[ASN][1000 genomes]
rs28847138	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3813603	0.85[ASN][1000 genomes]
rs485987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs551786	0.92[EUR][1000 genomes]
rs58489234	0.83[ASN][1000 genomes]
rs61164145	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv441699	chr1:85911291-85915402	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85893800-85916800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:85899200-85914800	Weak transcription	Esophagus	oesophagus
3	chr1:85901400-85923000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:85904400-85914800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:85905200-85914800	Weak transcription	Small Intestine	intestine
6	chr1:85907000-85914600	Weak transcription	Fetal Stomach	stomach
7	chr1:85907000-85914800	Weak transcription	Aorta	Aorta
8	chr1:85907000-85914800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:85907000-85919600	Weak transcription	Right Atrium	heart
10	chr1:85909200-85916600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:85910400-85916000	Weak transcription	HMEC	breast
12	chr1:85910600-85914800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:85911200-85917200	Enhancers	NHDF-Ad	bronchial
14	chr1:85911400-85914800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:85911400-85915000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:85911800-85916600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:85912000-85914600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:85912200-85914800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:85912200-85914800	Enhancers	NHLF	lung
20	chr1:85912200-85915600	Genic enhancers	HSMM	muscle
21	chr1:85912200-85916000	Enhancers	Liver	Liver
22	chr1:85912200-85917400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr1:85912400-85914800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:85912400-85915400	Enhancers	Brain Anterior Caudate	brain
25	chr1:85912800-85914800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:85912800-85915000	Enhancers	NH-A	brain
27	chr1:85912800-85915800	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr1:85912800-85916000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:85913000-85914800	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:85913000-85914800	Weak transcription	Pancreas	Pancrea
31	chr1:85913400-85914600	Enhancers	Fetal Lung	lung
32	chr1:85913400-85914800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:85913400-85914800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:85913400-85914800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:85913400-85915400	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr1:85913400-85917800	Weak transcription	Fetal Kidney	kidney
37	chr1:85913800-85914800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:85913800-85914800	Weak transcription	Adipose Nuclei	Adipose
39	chr1:85913800-85914800	Weak transcription	Left Ventricle	heart
40	chr1:85913800-85914800	Weak transcription	Psoas Muscle	Psoas
41	chr1:85913800-85914800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:85913800-85914800	Weak transcription	Spleen	Spleen
43	chr1:85913800-85914800	Enhancers	Osteobl	bone
44	chr1:85913800-85915000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:85913800-85915400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:85913800-85916600	Weak transcription	Fetal Intestine Small	intestine
47	chr1:85913800-85916800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:85913800-85916800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:85913800-85916800	Weak transcription	Right Ventricle	heart
50	chr1:85913800-85918400	Weak transcription	Colon Smooth Muscle	Colon

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