Variant report

Variant	rs1562325
Chromosome Location	chr11:36321379-36321380
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:36319061..36322401-chr11:36325495..36327520,3	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10836528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10836530	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10836531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11033538	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11033542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11602024	0.84[EUR][1000 genomes]
rs12294763	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs1562326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1562327	0.88[LWK][hapmap];0.81[EUR][1000 genomes]
rs17814690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2422185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2422186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2422187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2901672	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56386213	0.82[EUR][1000 genomes]
rs61878683	0.82[EUR][1000 genomes]
rs72946165	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1562325	LINC00610	cis	Thyroid	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36311400-36322600	Weak transcription	Spleen	Spleen
2	chr11:36311400-36331400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:36311600-36325800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr11:36311800-36321800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr11:36318000-36321800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:36318200-36322400	Weak transcription	Placenta	Placenta
7	chr11:36318800-36321800	Weak transcription	Fetal Lung	lung
8	chr11:36319200-36331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:36319400-36321600	Weak transcription	Colonic Mucosa	Colon
10	chr11:36319600-36321800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr11:36319600-36321800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr11:36319600-36322000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr11:36319600-36323400	Enhancers	Brain Angular Gyrus	brain
14	chr11:36319800-36321800	Weak transcription	Brain Anterior Caudate	brain
15	chr11:36319800-36321800	Weak transcription	Small Intestine	intestine
16	chr11:36319800-36321800	Weak transcription	Hela-S3	cervix
17	chr11:36320000-36323200	Enhancers	Brain Substantia Nigra	brain
18	chr11:36320400-36321600	Weak transcription	Adipose Nuclei	Adipose
19	chr11:36320400-36322000	Enhancers	Brain Hippocampus Middle	brain
20	chr11:36320600-36322200	Weak transcription	Fetal Intestine Small	intestine
21	chr11:36320800-36321800	Weak transcription	Fetal Intestine Large	intestine
22	chr11:36320800-36323000	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr11:36321000-36321400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr11:36321000-36321800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr11:36321000-36322600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr11:36321200-36323200	Enhancers	Brain Cingulate Gyrus	brain
27	chr11:36321200-36323400	Enhancers	Fetal Muscle Leg	muscle

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