Variant report

Variant	rs3789942
Chromosome Location	chr10:98131446-98131447
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98129908..98132885-chr10:98133498..98137488,4	K562	blood:

Variant related genes	Relation type
ENSG00000095587	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10748673	0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs10786277	0.82[CEU][hapmap];0.84[CHD][hapmap]
rs10786279	0.88[CEU][hapmap]
rs10786281	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10786282	0.89[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs10882773	0.82[CEU][hapmap];0.84[CHD][hapmap]
rs10882777	0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs10882778	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10882783	0.89[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs10882784	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188734	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11188735	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11188736	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11188740	0.88[CHB][hapmap];0.91[CHD][hapmap];0.87[ASN][1000 genomes]
rs11188741	0.90[MEX][hapmap]
rs11818883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11818896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11818942	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1923707	0.82[CEU][hapmap];0.84[CHD][hapmap]
rs1923708	0.82[CEU][hapmap]
rs2146394	0.82[CEU][hapmap]
rs2154183	0.82[CEU][hapmap]
rs2273891	0.84[CHD][hapmap]
rs2861572	1.00[JPT][hapmap]
rs2901990	0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs3814223	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs3818313	0.84[CHD][hapmap]
rs4917732	1.00[JPT][hapmap]
rs61741039	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7077344	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7893551	0.89[CEU][hapmap]

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	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv831950	chr10:98080972-98245434	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1047657	chr10:98123234-98183487	Weak transcription Active TSS Genic enhancers Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3789942	CHUK	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98117000-98134400	Weak transcription	Thymus	Thymus
2	chr10:98127400-98133800	Weak transcription	Fetal Brain Female	brain
3	chr10:98128000-98133400	Weak transcription	Right Ventricle	heart
4	chr10:98128200-98134800	Weak transcription	Left Ventricle	heart
5	chr10:98128600-98133800	Weak transcription	Brain Angular Gyrus	brain
6	chr10:98129000-98133600	Weak transcription	Brain Hippocampus Middle	brain
7	chr10:98130000-98132200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr10:98130200-98131600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr10:98130200-98134400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr10:98130400-98134000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr10:98130400-98134800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr10:98130600-98134400	Weak transcription	A549	lung
13	chr10:98130600-98134600	Weak transcription	Pancreas	Pancrea
14	chr10:98130600-98134800	Weak transcription	Hela-S3	cervix
15	chr10:98130800-98133800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr10:98130800-98133800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr10:98130800-98134200	Weak transcription	Brain Anterior Caudate	brain
18	chr10:98130800-98134200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr10:98130800-98134400	Weak transcription	Brain Substantia Nigra	brain
20	chr10:98130800-98134600	Weak transcription	Dnd41	blood
21	chr10:98130800-98134800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr10:98131200-98134400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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