Variant report

Variant	rs12620501
Chromosome Location	chr2:30366649-30366650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30361415..30365100-chr2:30365958..30368991,4	K562	blood:
2	chr2:30366474..30375732-chr2:30375765..30384167,14	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ALK-1	chr2:30363506-30366670	ENSG00000233862.1

Variant related genes	Relation type
ENSG00000233862	Chromatin interaction
ENSG00000119801	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11127257	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11127258	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1137288	0.89[EUR][1000 genomes]
rs11688623	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11690964	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11903016	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12991494	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13017699	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17734800	0.99[ASN][1000 genomes]
rs17734815	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276548	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2361753	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34125526	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34350694	0.93[ASN][1000 genomes]
rs35466989	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35640159	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3768667	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4465805	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55869928	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62141084	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62141087	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62141088	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6747196	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7600457	0.89[EUR][1000 genomes]
rs7603324	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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	32 gene(s)	inside rSNPs	diseases
2	nsv1002657	chr2:30339312-30516535	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription 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	10 gene(s)	inside rSNPs	diseases
3	esv1794716	chr2:30356661-30370785	Active TSS Weak transcription Flanking Active TSS 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	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30358000-30368600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:30362400-30367000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:30362400-30367600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr2:30362400-30367600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:30362400-30367600	Weak transcription	Fetal Thymus	thymus
6	chr2:30362400-30367800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:30362400-30368600	Weak transcription	Thymus	Thymus
8	chr2:30362600-30367600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:30362600-30367600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:30362600-30367800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:30362800-30367600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:30362800-30367800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr2:30362800-30368000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:30362800-30368600	Weak transcription	GM12878-XiMat	blood
15	chr2:30362800-30368600	Weak transcription	HMEC	breast
16	chr2:30363000-30368400	Weak transcription	NHEK	skin
17	chr2:30363000-30368600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:30363200-30368600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:30363200-30368600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:30366200-30368600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr2:30366400-30368600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr2:30366600-30367800	Weak transcription	Primary T cells from cord blood	blood
23	chr2:30366600-30368600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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