Variant report

Variant	rs12268038
Chromosome Location	chr10:4990993-4990994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:4984421..4986595-chr10:4988529..4991058,2	K562	blood:
2	chr10:4867202..4868971-chr10:4989906..4992668,2	MCF-7	breast:
3	chr10:4990354..4992501-chr10:4997441..4999294,2	K562	blood:
4	chr10:4990497..4992169-chr10:4993252..4995468,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165568	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10795213	0.82[CEU][hapmap]
rs11252834	0.85[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs11252835	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2904802	0.81[CEU][hapmap]
rs3812666	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3812667	0.96[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3902925	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs4255441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4323780	0.81[CEU][hapmap]
rs4339935	0.89[CHB][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.84[AMR][1000 genomes]
rs4342925	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4364963	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4427477	0.85[CEU][hapmap]
rs4483487	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4528219	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4550138	0.89[CEU][hapmap]
rs4596966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4626969	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601872	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6601875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601876	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7076643	0.85[CEU][hapmap]
rs7076792	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7081421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7093917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096506	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7100824	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7901384	0.92[CEU][hapmap];0.83[CHB][hapmap];0.80[GIH][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7914666	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7921514	0.83[ASW][hapmap];0.92[CEU][hapmap];0.82[GIH][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8181448	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv948794	chr10:4863093-5227382	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1045155	chr10:4872239-5211318	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040343	chr10:4872814-5196815	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540462	chr10:4872814-5196815	Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv869470	chr10:4878904-5203685	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv466713	chr10:4901798-5319679	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv549881	chr10:4901798-5319679	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv1050246	chr10:4927428-5211318	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv549882	chr10:4943518-5203864	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv2763913	chr10:4961021-5321407	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv894794	chr10:4972761-5121745	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv430122	chr10:4986040-5134511	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12268038	AKR1C1	cis	Whole Blood	GTEx
rs12268038	C9orf43	trans	cerebellum	SCAN
rs12268038	ATP5C1	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4973000-5005600	Weak transcription	Left Ventricle	heart
2	chr10:4973200-4994800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr10:4983600-4991600	Enhancers	Adipose Nuclei	Adipose
4	chr10:4987200-4991000	Enhancers	Fetal Intestine Small	intestine
5	chr10:4987400-4991000	Enhancers	Fetal Intestine Large	intestine
6	chr10:4988000-4991200	Enhancers	Hela-S3	cervix
7	chr10:4989000-4991000	Enhancers	Colon Smooth Muscle	Colon
8	chr10:4989000-4991000	Enhancers	Stomach Mucosa	stomach
9	chr10:4989000-4991000	Flanking Active TSS	A549	lung
10	chr10:4989400-4991000	Enhancers	Rectal Smooth Muscle	rectum
11	chr10:4989400-4991600	Enhancers	Stomach Smooth Muscle	stomach
12	chr10:4989600-4991600	Enhancers	NHDF-Ad	bronchial
13	chr10:4989800-4991200	Enhancers	NHLF	lung
14	chr10:4990000-4991200	Enhancers	Brain Anterior Caudate	brain
15	chr10:4990000-4991200	Enhancers	Osteobl	bone
16	chr10:4990000-4991600	Enhancers	Small Intestine	intestine
17	chr10:4990000-4993200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr10:4990200-4991000	Enhancers	Fetal Stomach	stomach
19	chr10:4990200-4991000	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr10:4990200-4991200	Enhancers	Liver	Liver
21	chr10:4990200-4991600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr10:4990400-4991000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr10:4990400-4991200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr10:4990400-4991200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr10:4990400-4991200	Enhancers	Pancreas	Pancrea
26	chr10:4990400-4991400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr10:4990400-4991400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr10:4990600-4991000	Enhancers	Aorta	Aorta
29	chr10:4990600-4991000	Enhancers	Esophagus	oesophagus
30	chr10:4990600-4991200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr10:4990800-4991000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr10:4990800-4991200	Weak transcription	Right Atrium	heart
33	chr10:4990800-4994200	Enhancers	HepG2	liver
34	chr10:4990800-4999200	Weak transcription	HMEC	breast
35	chr10:4990800-5003800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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