Variant report

Variant	rs12526419
Chromosome Location	chr6:68750550-68750551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:68749500..68752266-chr6:69373788..69375882,2	K562	blood:
2	chr6:68750041..68751555-chr6:68934848..68937816,2	K562	blood:
3	chr6:68592757..68600938-chr6:68750277..68758089,29	K562	blood:
4	chr6:68589241..68603169-chr6:68747484..68757867,45	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BAI3-2	chr6:68750266-68750833	XLOC_005339
2	lnc-BAI3-2	chr6:68750164-68751894	NONHSAT113395

Variant related genes	Relation type
ENSG00000227706	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10945052	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193704	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12201957	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12202242	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12204709	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12526505	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13204707	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13207384	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1350024	0.92[ASN][1000 genomes]
rs1378451	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378455	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378456	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1455444	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1531064	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168292	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35506850	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs36102084	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3964402	0.92[ASN][1000 genomes]
rs4574592	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6905781	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6934565	0.88[ASN][1000 genomes]
rs7743527	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751480	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7767069	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9363849	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027923	chr6:67830533-68828337	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv603589	chr6:67975166-68865718	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv3415097	chr6:68536406-69244164	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv886128	chr6:68707131-68783499	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
5	nsv1016113	chr6:68708308-69059884	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv538298	chr6:68708308-69059884	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv2752129	chr6:68731109-69033568	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1020734	chr6:68739118-69128457	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv538299	chr6:68739118-69128457	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv886129	chr6:68739602-68783499	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
11	nsv603605	chr6:68739602-69135009	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1033280	chr6:68740954-69105022	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:68748200-68751000	Enhancers	H9 Cell Line	embryonic stem cell
2	chr6:68748400-68752000	Enhancers	H1 Cell Line	embryonic stem cell
3	chr6:68749000-68751000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:68749200-68750600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr6:68749200-68751000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr6:68749200-68751000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr6:68749200-68751000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr6:68749400-68751000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr6:68749800-68750600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:68749800-68751000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:68749800-68756400	Active TSS	K562	blood
12	chr6:68750000-68751000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:68750000-68751000	Active TSS	Brain Substantia Nigra	brain
14	chr6:68750000-68751000	Active TSS	NH-A	brain
15	chr6:68750000-68751200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr6:68750000-68751600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr6:68750200-68750600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr6:68750200-68750600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:68750200-68750600	Active TSS	Brain Angular Gyrus	brain
20	chr6:68750200-68750600	Active TSS	Brain Cingulate Gyrus	brain
21	chr6:68750200-68750600	Active TSS	Brain Germinal Matrix	brain
22	chr6:68750200-68750600	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr6:68750200-68750600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:68750200-68750600	Active TSS	Fetal Lung	lung
25	chr6:68750200-68750600	Active TSS	Monocytes-CD14+_RO01746	blood
26	chr6:68750200-68750800	Active TSS	Adipose Nuclei	Adipose
27	chr6:68750200-68750800	Active TSS	Brain Anterior Caudate	brain
28	chr6:68750200-68750800	Active TSS	Brain Hippocampus Middle	brain
29	chr6:68750200-68750800	Active TSS	Hela-S3	cervix
30	chr6:68750200-68751000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:68750200-68751000	Active TSS	Primary B cells from cord blood	blood
32	chr6:68750200-68751000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:68750200-68751000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:68750200-68751000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:68750200-68751000	Active TSS	Left Ventricle	heart
36	chr6:68750200-68751000	Active TSS	Right Atrium	heart
37	chr6:68750200-68751200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:68750200-68751200	Active TSS	Fetal Kidney	kidney
39	chr6:68750400-68750800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:68750400-68750800	Active TSS	Primary hematopoietic stem cells	blood
41	chr6:68750400-68750800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:68750400-68750800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:68750400-68751000	Active TSS	Fetal Muscle Leg	muscle
44	chr6:68750400-68751000	Active TSS	Fetal Thymus	thymus

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