Variant report

Variant	rs2430940
Chromosome Location	chr12:46944794-46944795
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46775028..46778890-chr12:46944672..46947294,3	K562	blood:
2	chr12:46944404..46946357-chr12:46950000..46951515,2	K562	blood:
3	chr12:46942932..46945589-chr12:46948248..46950851,2	MCF-7	breast:
4	chr12:46766323..46768066-chr12:46942252..46945383,3	K562	blood:
5	chr12:46941171..46945201-chr12:46945236..46949422,7	K562	blood:
6	chr12:46661429..46663096-chr12:46943395..46946017,2	K562	blood:
7	chr12:46775028..46778890-chr12:46944542..46947294,5	K562	blood:
8	chr12:46661324..46663947-chr12:46944457..46946372,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257261	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 157 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:152)

rs_ID	r²[population]
rs10785631	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs10880975	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10880976	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes]
rs10880977	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10880980	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11183464	1.00[CEU][hapmap]
rs11183497	1.00[CEU][hapmap]
rs11183507	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11183524	1.00[EUR][1000 genomes]
rs11183527	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11183536	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11183539	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11183547	0.93[EUR][1000 genomes]
rs11183550	0.93[EUR][1000 genomes]
rs11829502	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11830099	0.95[EUR][1000 genomes]
rs11830501	0.95[EUR][1000 genomes]
rs11831177	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs11831920	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11831929	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11832316	0.95[EUR][1000 genomes]
rs11833393	1.00[EUR][1000 genomes]
rs11834607	1.00[EUR][1000 genomes]
rs11835517	0.95[EUR][1000 genomes]
rs11835974	0.95[EUR][1000 genomes]
rs11836915	1.00[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs11836940	1.00[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]
rs11837104	0.95[EUR][1000 genomes]
rs12300125	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12301825	0.87[MEX][hapmap]
rs12305921	1.00[CEU][hapmap]
rs12310635	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12578813	0.88[EUR][1000 genomes]
rs12579089	0.88[EUR][1000 genomes]
rs12579348	0.95[EUR][1000 genomes]
rs12579976	0.95[EUR][1000 genomes]
rs12580092	0.95[EUR][1000 genomes]
rs12580121	1.00[CEU][hapmap]
rs12580356	0.88[EUR][1000 genomes]
rs12580488	0.85[EUR][1000 genomes]
rs12581311	0.88[EUR][1000 genomes]
rs12581366	0.88[EUR][1000 genomes]
rs12582013	0.85[EUR][1000 genomes]
rs12582056	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12582476	0.88[EUR][1000 genomes]
rs17096991	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17096995	1.00[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]
rs17097002	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17097009	0.95[EUR][1000 genomes]
rs17097022	1.00[CEU][hapmap];0.81[GIH][hapmap];0.95[EUR][1000 genomes]
rs17121410	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17121412	1.00[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]
rs17594275	0.85[EUR][1000 genomes]
rs17611638	0.88[EUR][1000 genomes]
rs1946175	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2042058	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2193662	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2193663	0.95[EUR][1000 genomes]
rs2216439	0.91[EUR][1000 genomes]
rs235601	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs235602	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs235607	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs235610	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs235616	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs235617	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs235621	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs235622	1.00[CEU][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs235625	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs235626	1.00[CEU][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs235627	0.90[EUR][1000 genomes]
rs2408576	0.95[EUR][1000 genomes]
rs2408577	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2430937	1.00[EUR][1000 genomes]
rs2430939	1.00[EUR][1000 genomes]
rs2430941	1.00[EUR][1000 genomes]
rs2430942	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2430943	1.00[EUR][1000 genomes]
rs2430946	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2430947	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2471581	0.88[EUR][1000 genomes]
rs2471583	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2471588	1.00[EUR][1000 genomes]
rs2471594	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2471601	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2471602	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2471605	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2471608	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2471617	1.00[EUR][1000 genomes]
rs2471618	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28768973	1.00[EUR][1000 genomes]
rs2897969	0.91[EUR][1000 genomes]
rs2909411	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2960450	1.00[EUR][1000 genomes]
rs34008890	0.90[EUR][1000 genomes]
rs35096979	0.90[EUR][1000 genomes]
rs4073924	0.88[EUR][1000 genomes]
rs4604970	0.95[EUR][1000 genomes]
rs4768124	0.82[MEX][hapmap]
rs4768125	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768731	0.93[AMR][1000 genomes]
rs4768735	0.93[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs4768741	1.00[CEU][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs4768742	0.87[EUR][1000 genomes]
rs4768744	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs56111534	0.87[EUR][1000 genomes]
rs56152575	0.95[EUR][1000 genomes]
rs56181923	0.95[EUR][1000 genomes]
rs56271434	0.95[EUR][1000 genomes]
rs56399247	0.88[EUR][1000 genomes]
rs57158113	0.88[EUR][1000 genomes]
rs57370043	0.90[EUR][1000 genomes]
rs57439008	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57658610	1.00[EUR][1000 genomes]
rs58449317	0.95[EUR][1000 genomes]
rs58503088	0.95[EUR][1000 genomes]
rs58561072	0.90[EUR][1000 genomes]
rs58813899	0.95[EUR][1000 genomes]
rs59521025	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59903937	0.95[EUR][1000 genomes]
rs60191997	1.00[EUR][1000 genomes]
rs60432604	0.88[EUR][1000 genomes]
rs60669661	0.95[EUR][1000 genomes]
rs60681792	0.95[EUR][1000 genomes]
rs61072098	0.97[EUR][1000 genomes]
rs61355826	1.00[EUR][1000 genomes]
rs61641663	0.90[EUR][1000 genomes]
rs6582666	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7138914	0.95[EUR][1000 genomes]
rs7295471	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7302876	0.86[EUR][1000 genomes]
rs7308386	0.95[EUR][1000 genomes]
rs7310326	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7310408	0.88[EUR][1000 genomes]
rs73282109	0.90[EUR][1000 genomes]
rs73290381	0.88[EUR][1000 genomes]
rs73290402	0.95[EUR][1000 genomes]
rs73291964	0.95[EUR][1000 genomes]
rs73291976	0.95[EUR][1000 genomes]
rs73291980	0.95[EUR][1000 genomes]
rs73292000	0.95[EUR][1000 genomes]
rs73292001	1.00[EUR][1000 genomes]
rs73293911	0.95[EUR][1000 genomes]
rs73293919	0.95[EUR][1000 genomes]
rs7484802	0.83[EUR][1000 genomes]
rs7488464	1.00[EUR][1000 genomes]
rs765707	0.95[EUR][1000 genomes]
rs766794	0.88[EUR][1000 genomes]
rs7976710	0.95[EUR][1000 genomes]
rs9669050	1.00[EUR][1000 genomes]
rs977069	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs9783500	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9971651	1.00[CEU][hapmap]

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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46928400-46948600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:46940000-46945600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:46940200-46945400	Enhancers	Muscle Satellite Cultured Cells	--
4	chr12:46940200-46950400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:46940200-46955000	Enhancers	HMEC	breast
6	chr12:46940600-46953600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:46940800-46947200	Enhancers	NHDF-Ad	bronchial
8	chr12:46941000-46949200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:46941400-46956200	Weak transcription	Primary B cells from cord blood	blood
10	chr12:46941800-46944800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr12:46942000-46947000	Weak transcription	Fetal Muscle Leg	muscle
12	chr12:46942400-46947000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:46942600-46947000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:46942600-46948200	Weak transcription	Adipose Nuclei	Adipose
15	chr12:46942800-46946200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:46942800-46946600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:46942800-46949400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:46943200-46947000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:46943400-46947000	Weak transcription	Psoas Muscle	Psoas
20	chr12:46943800-46945400	Enhancers	K562	blood
21	chr12:46943800-46946200	Weak transcription	Placenta	Placenta
22	chr12:46943800-46948600	Weak transcription	Fetal Heart	heart
23	chr12:46943800-46948800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:46944000-46946400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:46944000-46946800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:46944000-46947000	Weak transcription	HSMMtube	muscle
27	chr12:46944000-46948600	Enhancers	NHEK	skin
28	chr12:46944200-46945800	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr12:46944200-46946800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr12:46944200-46946800	Enhancers	A549	lung
31	chr12:46944200-46947000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr12:46944200-46947000	Weak transcription	HSMM	muscle
33	chr12:46944200-46947000	Weak transcription	NH-A	brain
34	chr12:46944200-46949400	Enhancers	Hela-S3	cervix
35	chr12:46944200-46949600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:46944400-46944800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:46944400-46946400	Weak transcription	NHLF	lung
38	chr12:46944400-46946600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:46944400-46946800	Weak transcription	HUVEC	blood vessel
40	chr12:46944400-46946800	Weak transcription	Osteobl	bone
41	chr12:46944600-46946200	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr12:46944600-46946600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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