Variant report

Variant	rs1253224
Chromosome Location	chr1:77693118-77693119
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77682598..77685827-chr1:77690810..77693587,3	K562	blood:
2	chr1:77690590..77694353-chr1:77694495..77697779,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AK5-2	chr1:77692452-77694222	NONHSAT004025

Variant related genes	Relation type
ENSG00000142892	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1098121	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1098129	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1098132	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1098133	0.80[AFR][1000 genomes]
rs1103683	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1253226	0.90[AFR][1000 genomes]
rs1266316	0.84[AFR][1000 genomes]
rs1270993	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12723684	0.87[AFR][1000 genomes]
rs12744696	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12746974	0.85[AMR][1000 genomes]
rs1419249	0.88[AFR][1000 genomes]
rs1502533	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1615806	0.80[AFR][1000 genomes]
rs1721127	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1721140	0.84[AFR][1000 genomes]
rs1721145	0.82[AFR][1000 genomes]
rs1721151	0.86[AFR][1000 genomes]
rs1779174	0.86[AFR][1000 genomes]
rs1779186	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1779189	0.84[AFR][1000 genomes]
rs1779198	0.82[AFR][1000 genomes]
rs2653469	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2689674	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2689675	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2689678	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2689679	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2762882	0.84[AFR][1000 genomes]
rs2799564	0.88[AFR][1000 genomes]
rs35446093	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67263641	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71658787	0.87[AFR][1000 genomes]
rs72681896	0.95[ASN][1000 genomes]
rs7524360	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs839799	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs839808	0.85[AFR][1000 genomes]
rs839810	0.85[AFR][1000 genomes]
rs839814	0.85[AFR][1000 genomes]
rs839818	0.85[AFR][1000 genomes]
rs839822	0.83[AFR][1000 genomes]
rs839823	0.85[AFR][1000 genomes]
rs839824	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs839826	0.80[AFR][1000 genomes]
rs839827	0.80[AFR][1000 genomes]
rs839830	0.80[AFR][1000 genomes]
rs839831	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs858447	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[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	nsv1006887	chr1:77566348-77698128	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv520629	chr1:77584846-77695854	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv525188	chr1:77655651-77695854	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr1:77685600-77693400	Weak transcription	Pancreas	Pancrea
2	chr1:77685800-77695600	Weak transcription	Left Ventricle	heart
3	chr1:77686000-77694600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:77686000-77694600	Weak transcription	Fetal Kidney	kidney
5	chr1:77686000-77699200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:77686600-77693200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:77686600-77694600	Weak transcription	A549	lung
8	chr1:77686600-77694800	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:77686600-77698200	Weak transcription	Brain Angular Gyrus	brain
10	chr1:77686800-77694600	Weak transcription	Brain Anterior Caudate	brain
11	chr1:77686800-77698000	Weak transcription	HUVEC	blood vessel
12	chr1:77687000-77695200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:77687000-77695200	Weak transcription	NHDF-Ad	bronchial
14	chr1:77687000-77695400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:77688400-77694200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:77688400-77697600	Weak transcription	Primary T cells from cord blood	blood
17	chr1:77690800-77695400	Weak transcription	HSMM	muscle
18	chr1:77692800-77693400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr1:77692800-77693800	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr1:77692800-77694800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr1:77693000-77693200	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr1:77693000-77693200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:77693000-77693600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:77693000-77693800	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr1:77693000-77693800	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr1:77693000-77695600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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