Variant report

Variant	rs9397541
Chromosome Location	chr6:150322211-150322212
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150320978..150322963-chr6:150324763..150326329,2	K562	blood:
2	chr6:150311706..150314148-chr6:150319764..150322563,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAET1L-2	chr6:150321989-150322804	NONHSAT115529

Variant related genes	Relation type
ENSG00000218358	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11155692	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11155693	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11964763	0.89[ASN][1000 genomes]
rs11967324	0.86[ASN][1000 genomes]
rs11967376	0.89[ASN][1000 genomes]
rs11967392	0.89[ASN][1000 genomes]
rs11969666	0.89[ASN][1000 genomes]
rs11969681	0.89[ASN][1000 genomes]
rs12191283	0.97[EUR][1000 genomes]
rs13192866	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13199630	0.90[ASN][1000 genomes]
rs13214660	0.89[ASN][1000 genomes]
rs1830833	0.90[ASN][1000 genomes]
rs1853666	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1853667	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1886363	0.83[ASN][1000 genomes]
rs1889553	0.80[ASN][1000 genomes]
rs1889554	0.82[ASN][1000 genomes]
rs2224893	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2275092	0.99[ASN][1000 genomes]
rs2343265	0.88[ASN][1000 genomes]
rs3860819	0.90[ASN][1000 genomes]
rs3888034	0.91[ASN][1000 genomes]
rs3963990	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4472362	0.88[ASN][1000 genomes]
rs6922028	0.92[EUR][1000 genomes]
rs6940683	0.95[ASN][1000 genomes]
rs7739781	0.90[ASN][1000 genomes]
rs7757868	0.96[EUR][1000 genomes]
rs7762217	0.98[ASN][1000 genomes]
rs9322232	0.90[ASN][1000 genomes]
rs9371624	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9383996	0.89[ASN][1000 genomes]
rs9384002	0.90[ASN][1000 genomes]
rs9384003	0.90[ASN][1000 genomes]
rs9384010	0.90[ASN][1000 genomes]
rs9384011	0.90[ASN][1000 genomes]
rs9384023	0.97[EUR][1000 genomes]
rs9384030	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9384033	0.99[ASN][1000 genomes]
rs9397517	0.89[ASN][1000 genomes]
rs9397521	0.89[ASN][1000 genomes]
rs942513	0.88[ASN][1000 genomes]
rs942514	0.88[ASN][1000 genomes]
rs9478336	0.89[ASN][1000 genomes]
rs9479328	0.90[ASN][1000 genomes]
rs9479329	0.90[ASN][1000 genomes]
rs9479330	0.90[ASN][1000 genomes]
rs9479331	0.90[ASN][1000 genomes]
rs9479332	0.90[ASN][1000 genomes]
rs9479339	0.89[ASN][1000 genomes]
rs9479340	0.89[ASN][1000 genomes]
rs9479341	0.89[ASN][1000 genomes]
rs9479343	0.90[ASN][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	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv970176	chr6:150319173-150343329	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr6:150315000-150324800	Weak transcription	Dnd41	blood
2	chr6:150318200-150325400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:150319000-150322600	Weak transcription	Thymus	Thymus
4	chr6:150319800-150325600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:150320800-150322400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:150320800-150324200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:150321400-150322400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr6:150321400-150325200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:150321600-150323200	Enhancers	Fetal Thymus	thymus
10	chr6:150321600-150325400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:150321800-150322600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:150321800-150322800	Enhancers	Primary T cells from cord blood	blood
13	chr6:150322000-150322400	Flanking Active TSS	GM12878-XiMat	blood
14	chr6:150322000-150322600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:150322000-150322800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr6:150322000-150323200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:150322000-150323200	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr6:150322000-150323200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:150322000-150323400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr6:150322200-150322800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr6:150322200-150323000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr6:150322200-150323400	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr6:150322200-150323400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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