Variant report

Variant	rs4258438
Chromosome Location	chr12:46809126-46809127
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46804079..46806251-chr12:46809068..46811105,2	K562	blood:
2	chr12:46776981..46779414-chr12:46807717..46810201,3	MCF-7	breast:
3	chr12:46800362..46803961-chr12:46808441..46811398,3	K562	blood:
4	chr12:46777177..46779735-chr12:46808797..46811746,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC38A2-1	chr12:46808911-46809519	NONHSAT027862

Variant related genes	Relation type
ENSG00000257261	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10467213	0.82[AMR][1000 genomes]
rs10748448	0.82[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10748450	0.86[EUR][1000 genomes]
rs10785627	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10785628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10785629	0.86[EUR][1000 genomes]
rs1079780	0.84[AMR][1000 genomes]
rs10880961	0.80[AMR][1000 genomes]
rs10880966	0.90[AMR][1000 genomes]
rs10880967	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10880968	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10880969	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880970	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880971	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10880973	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11183456	1.00[CHB][hapmap]
rs11183478	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11183479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11183483	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11183484	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11183486	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11183488	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11183503	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11183504	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1125909	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11561535	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11837427	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12099669	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12298616	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12314541	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12319162	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12813763	0.84[AMR][1000 genomes]
rs12814341	0.84[AMR][1000 genomes]
rs12816358	0.84[AMR][1000 genomes]
rs12822345	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12824565	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12832425	0.84[AMR][1000 genomes]
rs12832777	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1472178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472179	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492895	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2045556	0.89[CHB][hapmap]
rs2131371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2220727	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2408497	0.89[AMR][1000 genomes]
rs2408498	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2408504	0.80[AMR][1000 genomes]
rs2408507	0.82[AMR][1000 genomes]
rs2897951	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2897968	0.81[AMR][1000 genomes]
rs3936214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4072304	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4076247	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4077707	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs4077708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs4427617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4586238	0.82[AMR][1000 genomes]
rs4768118	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4768119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768121	0.80[AMR][1000 genomes]
rs4768122	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4768696	0.84[AMR][1000 genomes]
rs4768699	0.86[CEU][hapmap]
rs4768704	0.82[AMR][1000 genomes]
rs4768709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768710	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768711	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4768712	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768713	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768714	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768715	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4768716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768717	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768718	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768719	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs4768724	0.86[EUR][1000 genomes]
rs4768725	0.86[EUR][1000 genomes]
rs4768726	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768728	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768729	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6582636	0.83[CEU][hapmap]
rs6582641	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6582642	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6582643	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6582645	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6582646	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582657	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6582658	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6582659	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7134289	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7301001	0.80[AMR][1000 genomes]
rs7311504	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7312259	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7485580	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7485599	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7486495	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7486532	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7486580	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7486596	0.80[EUR][1000 genomes]
rs7487828	0.85[AMR][1000 genomes]
rs7487877	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7488450	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7488577	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7489242	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7958774	0.82[AMR][1000 genomes]
rs7959731	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7968897	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976280	0.89[AMR][1000 genomes]
rs7979418	0.81[AMR][1000 genomes]
rs7980455	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9669404	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9706162	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9971879	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[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	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46795000-46809200	Weak transcription	Esophagus	oesophagus
2	chr12:46797000-46819800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:46799000-46809200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:46802000-46812200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:46803200-46809400	Weak transcription	Left Ventricle	heart
6	chr12:46804800-46809400	Weak transcription	Adipose Nuclei	Adipose
7	chr12:46806400-46812000	Weak transcription	Primary B cells from cord blood	blood
8	chr12:46807800-46809200	Enhancers	NHEK	skin
9	chr12:46807800-46809600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:46807800-46815600	Weak transcription	HepG2	liver
11	chr12:46808000-46810000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:46808000-46817200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:46808200-46809200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:46808400-46809400	Enhancers	HMEC	breast
15	chr12:46808600-46809800	Enhancers	Osteobl	bone
16	chr12:46808800-46809800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr12:46809000-46809600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:46809000-46810000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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