Variant report

Variant	rs1923704
Chromosome Location	chr10:98102398-98102399
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10218881	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748671	0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10786277	0.84[CEU][hapmap];0.87[TSI][hapmap]
rs10786280	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882773	0.88[ASW][hapmap];0.84[CEU][hapmap];0.87[TSI][hapmap]
rs10882775	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882779	0.80[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10882781	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11188722	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188724	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188725	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188726	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188731	0.85[JPT][hapmap]
rs12242936	0.81[JPT][hapmap]
rs12254238	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258764	0.81[GIH][hapmap]
rs12570008	0.81[JPT][hapmap]
rs12571241	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs12572329	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.99[ASN][1000 genomes]
rs17111736	0.81[JPT][hapmap]
rs1923706	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923707	0.88[ASW][hapmap];0.84[CEU][hapmap];0.87[TSI][hapmap]
rs1923708	0.84[CEU][hapmap]
rs2146392	0.87[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2146393	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146394	0.84[CEU][hapmap]
rs2154183	0.84[CEU][hapmap]
rs2861574	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901989	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3789938	0.85[GIH][hapmap]
rs3789942	0.81[TSI][hapmap]
rs3814224	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4424609	1.00[ASN][1000 genomes]
rs7085949	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096643	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7893551	0.80[CEU][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1923704	CHUK	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98100000-98103600	Weak transcription	Fetal Thymus	thymus
2	chr10:98100200-98103600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr10:98100200-98104200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr10:98100800-98104000	Strong transcription	Dnd41	blood
5	chr10:98100800-98105000	Strong transcription	Thymus	Thymus
6	chr10:98101200-98103800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr10:98101400-98105600	Weak transcription	Brain Anterior Caudate	brain
8	chr10:98101400-98105600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr10:98101600-98103600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr10:98101600-98104200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr10:98101600-98104800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr10:98101600-98104800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr10:98101600-98104800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr10:98101600-98104800	Weak transcription	Brain Substantia Nigra	brain
15	chr10:98101600-98105000	Weak transcription	Brain Hippocampus Middle	brain
16	chr10:98101600-98105400	Weak transcription	Brain Angular Gyrus	brain
17	chr10:98101600-98105600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr10:98101600-98105600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr10:98101800-98103600	Enhancers	Liver	Liver
20	chr10:98102000-98103600	Weak transcription	GM12878-XiMat	blood

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