Variant report

Variant	rs12631127
Chromosome Location	chr3:178974839-178974840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:178973918..178976093-chr3:178977084..178979092,2	MCF-7	breast:
2	chr3:178971723..178975105-chr3:178977726..178980619,4	K562	blood:
3	chr3:178973761..178975964-chr3:178977750..178980174,2	MCF-7	breast:
4	chr3:178861208..178863528-chr3:178973600..178975107,2	K562	blood:
5	chr3:178971723..178977145-chr3:178977567..178980865,6	K562	blood:

Variant related genes	Relation type
ENSG00000240429	Chromatin interaction
ENSG00000171121	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10804876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10804877	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10804878	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10804879	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10936995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11720871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11720935	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12633678	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12633724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1477190	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1968207	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1968208	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2864412	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56295844	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56400023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62410370	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62410371	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62410372	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62410373	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62410374	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6773405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7429685	0.98[ASN][1000 genomes]
rs7617552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7639338	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7642066	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	esv1800747	chr3:178962897-178977074	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv1010137	chr3:178962897-179050787	Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
11	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178912400-178978600	Weak transcription	Right Ventricle	heart
2	chr3:178945800-178978400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:178948800-178978600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:178949000-178978200	Weak transcription	NHLF	lung
5	chr3:178949000-178978600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:178949000-178978600	Weak transcription	Ovary	ovary
7	chr3:178949000-178978800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:178949200-178978400	Weak transcription	Brain Anterior Caudate	brain
9	chr3:178949200-178978600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:178949200-178978600	Weak transcription	Osteobl	bone
11	chr3:178952000-178978400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:178952400-178978600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr3:178952600-178976600	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:178956200-178977000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:178959800-178978800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:178963200-178978200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:178963200-178978600	Weak transcription	Left Ventricle	heart
18	chr3:178963200-178978800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:178963800-178978800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:178966200-178978600	Weak transcription	HUVEC	blood vessel
21	chr3:178968800-178978400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:178968800-178978600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:178969000-178975200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:178969200-178978400	Weak transcription	Primary B cells from cord blood	blood
25	chr3:178969400-178975600	Weak transcription	Gastric	stomach
26	chr3:178969400-178976600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:178969400-178978200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:178969600-178978600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:178972000-178978800	Weak transcription	Small Intestine	intestine
30	chr3:178974000-178975800	Enhancers	Pancreas	Pancrea
31	chr3:178974000-178976800	Active TSS	K562	blood
32	chr3:178974400-178977600	Active TSS	GM12878-XiMat	blood
33	chr3:178974800-178975000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr3:178974800-178975000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:178974800-178975000	Enhancers	Adipose Nuclei	Adipose
36	chr3:178974800-178975000	Enhancers	Spleen	Spleen
37	chr3:178974800-178975400	Enhancers	HepG2	liver

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