Variant report

Variant	rs4073924
Chromosome Location	chr12:46919978-46919979
allele	A/G
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46917446..46920289-chr12:46926732..46928567,2	K562	blood:
2	chr12:46914529..46916503-chr12:46919514..46921258,2	K562	blood:
3	chr12:46859540..46862018-chr12:46919142..46921108,2	K562	blood:
4	chr12:46912625..46916029-chr12:46919758..46923382,3	K562	blood:
5	chr12:46912402..46915807-chr12:46917000..46920176,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC38A2-3	chr12:46919938-46920055	NONHSAT027883

No data

Extended variants
information (count: 142 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs10785631	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10880975	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10880976	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs10880977	1.00[CEU][hapmap];0.80[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs10880980	1.00[EUR][1000 genomes]
rs11183464	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs11183497	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs11183507	0.85[EUR][1000 genomes]
rs11183510	0.81[CHD][hapmap]
rs11183524	0.88[EUR][1000 genomes]
rs11183536	0.88[EUR][1000 genomes]
rs11183539	0.81[EUR][1000 genomes]
rs11183547	0.81[EUR][1000 genomes]
rs11183550	0.81[EUR][1000 genomes]
rs11504523	0.85[EUR][1000 genomes]
rs11829502	1.00[CEU][hapmap];0.88[YRI][hapmap];0.98[EUR][1000 genomes]
rs11830099	0.93[EUR][1000 genomes]
rs11830501	0.93[EUR][1000 genomes]
rs11831177	1.00[CEU][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.85[EUR][1000 genomes]
rs11831920	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11831929	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11832316	0.93[EUR][1000 genomes]
rs11833393	0.88[EUR][1000 genomes]
rs11834607	0.88[EUR][1000 genomes]
rs11835517	0.93[EUR][1000 genomes]
rs11835974	0.93[EUR][1000 genomes]
rs11836915	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11836940	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[EUR][1000 genomes]
rs11837104	0.93[EUR][1000 genomes]
rs12300125	1.00[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs12305921	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs12578813	0.85[EUR][1000 genomes]
rs12579089	0.85[EUR][1000 genomes]
rs12579348	0.93[EUR][1000 genomes]
rs12579976	0.93[EUR][1000 genomes]
rs12580092	0.83[EUR][1000 genomes]
rs12580121	1.00[CEU][hapmap]
rs12580356	0.85[EUR][1000 genomes]
rs12580488	0.82[EUR][1000 genomes]
rs12581311	0.82[EUR][1000 genomes]
rs12581366	0.85[EUR][1000 genomes]
rs12582013	0.82[EUR][1000 genomes]
rs12582056	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12582476	0.85[EUR][1000 genomes]
rs17096991	1.00[CEU][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes]
rs17096995	1.00[CEU][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17097002	1.00[CEU][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes]
rs17097009	0.93[EUR][1000 genomes]
rs17097022	1.00[CEU][hapmap];0.88[YRI][hapmap];0.93[EUR][1000 genomes]
rs17121410	0.82[ASW][hapmap];1.00[CEU][hapmap];0.87[TSI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17121412	1.00[CEU][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[EUR][1000 genomes]
rs17594275	0.82[EUR][1000 genomes]
rs17611638	0.85[EUR][1000 genomes]
rs1946175	0.88[EUR][1000 genomes]
rs2042058	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2193663	0.93[EUR][1000 genomes]
rs2216439	0.90[EUR][1000 genomes]
rs235601	0.81[EUR][1000 genomes]
rs235602	0.81[EUR][1000 genomes]
rs235607	1.00[CEU][hapmap]
rs235610	0.81[EUR][1000 genomes]
rs235617	1.00[CEU][hapmap]
rs235621	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs235622	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs235626	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs2408576	0.93[EUR][1000 genomes]
rs2408577	0.88[EUR][1000 genomes]
rs2430937	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2430939	0.88[EUR][1000 genomes]
rs2430940	1.00[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs2430941	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2430942	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2430943	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2430946	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2430947	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes]
rs2471581	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2471583	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[EUR][1000 genomes]
rs2471588	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2471594	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2471601	0.88[EUR][1000 genomes]
rs2471602	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2471605	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2471608	1.00[CEU][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes]
rs2471617	0.88[EUR][1000 genomes]
rs2471618	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs28768973	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2897969	0.89[EUR][1000 genomes]
rs2909411	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2960450	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4604970	0.93[EUR][1000 genomes]
rs4768125	0.80[EUR][1000 genomes]
rs4768731	0.82[EUR][1000 genomes]
rs4768741	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs4768744	1.00[CEU][hapmap]
rs56152575	0.93[EUR][1000 genomes]
rs56181923	0.93[EUR][1000 genomes]
rs56271434	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56399247	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57158113	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57439008	0.85[EUR][1000 genomes]
rs57658610	0.88[EUR][1000 genomes]
rs58449317	0.93[EUR][1000 genomes]
rs58503088	0.93[EUR][1000 genomes]
rs58813899	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59521025	0.85[EUR][1000 genomes]
rs59903937	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs60191997	0.88[EUR][1000 genomes]
rs60432604	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60669661	0.93[EUR][1000 genomes]
rs60681792	0.93[EUR][1000 genomes]
rs61072098	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs61355826	0.88[EUR][1000 genomes]
rs6582666	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7138914	0.93[EUR][1000 genomes]
rs7295471	1.00[CEU][hapmap];0.80[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs7302876	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7308386	0.93[EUR][1000 genomes]
rs7310326	1.00[CEU][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes]
rs73290364	0.81[EUR][1000 genomes]
rs73290381	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73290402	0.93[EUR][1000 genomes]
rs73291964	0.93[EUR][1000 genomes]
rs73291976	0.93[EUR][1000 genomes]
rs73291980	0.93[EUR][1000 genomes]
rs73292000	0.93[EUR][1000 genomes]
rs73292001	0.88[EUR][1000 genomes]
rs73293911	0.93[EUR][1000 genomes]
rs73293919	0.93[EUR][1000 genomes]
rs74085431	0.85[EUR][1000 genomes]
rs7488464	0.88[EUR][1000 genomes]
rs765707	0.93[EUR][1000 genomes]
rs766794	0.85[EUR][1000 genomes]
rs7953339	0.81[CHD][hapmap]
rs7976710	0.93[EUR][1000 genomes]
rs9669050	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs977069	1.00[CEU][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs9783500	0.85[EUR][1000 genomes]
rs9971651	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46910800-46920000	Enhancers	Fetal Lung	lung
2	chr12:46911600-46922800	Weak transcription	Primary B cells from cord blood	blood
3	chr12:46911800-46921800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr12:46913600-46921400	Weak transcription	GM12878-XiMat	blood
5	chr12:46916200-46920400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr12:46916400-46921000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:46916800-46920000	Enhancers	Fetal Thymus	thymus
8	chr12:46917000-46920800	Enhancers	Fetal Muscle Leg	muscle
9	chr12:46917200-46920000	Enhancers	Left Ventricle	heart
10	chr12:46917800-46920000	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr12:46917800-46920400	Enhancers	Ovary	ovary
12	chr12:46918000-46920400	Enhancers	Psoas Muscle	Psoas
13	chr12:46918000-46924800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:46918400-46924200	Weak transcription	Right Ventricle	heart
15	chr12:46918600-46920000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr12:46918600-46920000	Enhancers	HSMMtube	muscle
17	chr12:46918800-46920200	Enhancers	Colon Smooth Muscle	Colon
18	chr12:46918800-46925000	Weak transcription	NHEK	skin
19	chr12:46919000-46922000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:46919000-46922600	Weak transcription	Pancreas	Pancrea
21	chr12:46919000-46924800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:46919200-46920000	Enhancers	HSMM	muscle
23	chr12:46919200-46929800	Weak transcription	A549	lung
24	chr12:46919400-46929400	Weak transcription	Right Atrium	heart
25	chr12:46919600-46924000	Weak transcription	Fetal Stomach	stomach
26	chr12:46919800-46927600	Weak transcription	Fetal Heart	heart

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