Variant report

Variant	rs2430941
Chromosome Location	chr12:46949722-46949723
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46765672..46767506-chr12:46948765..46951182,2	MCF-7	breast:
2	chr12:46949570..46952238-chr12:47068920..47070785,2	K562	blood:
3	chr12:46748960..46751313-chr12:46947807..46949856,2	MCF-7	breast:
4	chr12:46942932..46945589-chr12:46948248..46950851,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10880980	0.88[EUR][1000 genomes]
rs11183524	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11183536	1.00[EUR][1000 genomes]
rs11183539	0.93[EUR][1000 genomes]
rs11183547	0.93[EUR][1000 genomes]
rs11183550	0.93[EUR][1000 genomes]
rs11829502	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11830099	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11830501	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11831920	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11831929	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11832316	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11833393	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11834607	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11835517	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11835974	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11836915	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11836940	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11837104	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12300125	1.00[EUR][1000 genomes]
rs12310635	0.84[EUR][1000 genomes]
rs12578813	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12579089	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12579348	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12579976	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12580092	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12580356	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12580488	0.85[EUR][1000 genomes]
rs12581311	0.88[EUR][1000 genomes]
rs12581366	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12582013	0.85[EUR][1000 genomes]
rs12582056	0.93[EUR][1000 genomes]
rs12582476	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17096991	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17096995	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17097002	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17097009	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17097022	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17121410	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17121412	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17594275	0.85[EUR][1000 genomes]
rs17611638	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1946175	1.00[EUR][1000 genomes]
rs2042058	0.88[EUR][1000 genomes]
rs2193662	0.91[EUR][1000 genomes]
rs2193663	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2216439	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs235601	0.93[EUR][1000 genomes]
rs235602	0.93[EUR][1000 genomes]
rs235607	0.90[EUR][1000 genomes]
rs235610	0.93[EUR][1000 genomes]
rs235616	0.86[EUR][1000 genomes]
rs235621	0.90[EUR][1000 genomes]
rs235622	0.90[EUR][1000 genomes]
rs235625	0.90[EUR][1000 genomes]
rs235626	0.90[EUR][1000 genomes]
rs235627	0.90[EUR][1000 genomes]
rs2408576	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2408577	1.00[EUR][1000 genomes]
rs2430937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2430939	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2430940	1.00[EUR][1000 genomes]
rs2430942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2430943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2430946	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2430947	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2471581	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2471583	0.88[EUR][1000 genomes]
rs2471588	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2471594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2471601	1.00[EUR][1000 genomes]
rs2471602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2471605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2471608	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2471617	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2471618	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28768973	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2897969	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2909411	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2960450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34008890	0.90[EUR][1000 genomes]
rs35096979	0.90[EUR][1000 genomes]
rs4073924	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4604970	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768125	0.93[EUR][1000 genomes]
rs4768741	0.81[EUR][1000 genomes]
rs4768742	0.87[EUR][1000 genomes]
rs4768744	0.88[EUR][1000 genomes]
rs56111534	0.87[EUR][1000 genomes]
rs56152575	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56181923	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56271434	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56399247	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57158113	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs57370043	0.90[EUR][1000 genomes]
rs57658610	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58449317	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58503088	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58561072	0.90[EUR][1000 genomes]
rs58813899	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59903937	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60191997	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60432604	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60669661	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60681792	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61072098	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61355826	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61641663	0.90[EUR][1000 genomes]
rs7138914	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302876	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7308386	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7310326	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7310408	0.88[EUR][1000 genomes]
rs73282109	0.90[EUR][1000 genomes]
rs73290381	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73290402	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73291964	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73291976	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73291980	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73292000	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73292001	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73293911	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73293919	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7484802	0.83[EUR][1000 genomes]
rs7488464	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs765707	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs766794	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7976710	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9669050	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs977069	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases
5	esv3402095	chr12:46937340-46983181	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46940200-46950400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:46940200-46955000	Enhancers	HMEC	breast
3	chr12:46940600-46953600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:46941400-46956200	Weak transcription	Primary B cells from cord blood	blood
5	chr12:46947000-46950000	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr12:46947200-46950000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:46947200-46956000	Weak transcription	Left Ventricle	heart
8	chr12:46947400-46949800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:46948200-46952400	Enhancers	Adipose Nuclei	Adipose
10	chr12:46948400-46950200	Enhancers	Fetal Kidney	kidney
11	chr12:46948600-46950600	Enhancers	Rectal Smooth Muscle	rectum
12	chr12:46948600-46954200	Enhancers	Colon Smooth Muscle	Colon
13	chr12:46948800-46949800	Enhancers	Fetal Muscle Leg	muscle
14	chr12:46948800-46949800	Enhancers	Psoas Muscle	Psoas
15	chr12:46948800-46950000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:46948800-46950000	Enhancers	Fetal Intestine Large	intestine
17	chr12:46948800-46950200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr12:46948800-46950400	Enhancers	Fetal Stomach	stomach
19	chr12:46949000-46954000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:46949000-46954000	Weak transcription	Aorta	Aorta
21	chr12:46949200-46949800	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr12:46949200-46949800	Flanking Active TSS	Fetal Lung	lung
23	chr12:46949200-46950000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:46949200-46950000	Flanking Active TSS	Osteobl	bone
25	chr12:46949200-46950200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:46949200-46950200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:46949200-46950400	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr12:46949200-46950400	Enhancers	K562	blood
29	chr12:46949200-46951000	Enhancers	HUVEC	blood vessel
30	chr12:46949400-46949800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:46949400-46949800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:46949400-46949800	Flanking Active TSS	Fetal Heart	heart
33	chr12:46949400-46949800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr12:46949400-46949800	Flanking Active TSS	NHLF	lung
35	chr12:46949400-46950000	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr12:46949400-46950000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:46949400-46950000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr12:46949400-46950000	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr12:46949400-46950000	Flanking Active TSS	Hela-S3	cervix
40	chr12:46949400-46950000	Flanking Active TSS	HSMM	muscle
41	chr12:46949400-46950000	Flanking Active TSS	NH-A	brain
42	chr12:46949400-46950000	Flanking Active TSS	NHDF-Ad	bronchial
43	chr12:46949400-46950200	Enhancers	HepG2	liver
44	chr12:46949400-46950400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:46949400-46950400	Enhancers	Liver	Liver
46	chr12:46949400-46954400	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr12:46949600-46950000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:46949600-46950000	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr12:46949600-46950000	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr12:46949600-46950000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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