Variant report

Variant	rs1242062
Chromosome Location	chr3:143375977-143375978
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	chr3:143366241..143367963-chr3:143375379..143377183,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf58-2	chr3:143372169-143376642	NONHSAT092529

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1242047	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1242048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1242051	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1242052	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1242053	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1242055	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1242059	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1242060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1242063	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1242069	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1242071	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1242072	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1242078	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1242080	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1268369	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1270765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1447736	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1447737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1447739	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17639455	1.00[ASW][hapmap]
rs1868176	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6782176	1.00[CEU][hapmap]
rs73152842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73152843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73152844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73152845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7648523	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7653163	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs935518	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9877738	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv829745	chr3:143278512-143405626	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143328200-143376200	Weak transcription	Ovary	ovary
2	chr3:143363400-143377600	Weak transcription	NHDF-Ad	bronchial
3	chr3:143363600-143377800	Weak transcription	Adipose Nuclei	Adipose
4	chr3:143363600-143379000	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:143367400-143390400	Weak transcription	Brain Substantia Nigra	brain
6	chr3:143370200-143376000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:143370400-143390400	Weak transcription	Fetal Lung	lung
8	chr3:143370800-143420800	Weak transcription	Primary T cells from cord blood	blood
9	chr3:143371200-143383000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr3:143374200-143382800	Weak transcription	Esophagus	oesophagus
11	chr3:143374400-143377200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:143374600-143376000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr3:143374600-143377800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr3:143374600-143378600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:143374800-143376200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:143374800-143376200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr3:143374800-143376200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:143375000-143376000	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr3:143375000-143376400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr3:143375000-143377600	Weak transcription	HMEC	breast
21	chr3:143375200-143376000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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