Variant report

Variant	rs701814
Chromosome Location	chr10:98975719-98975720
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11189052	0.81[EUR][1000 genomes]
rs11189121	0.95[CEU][hapmap];0.84[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs1147600	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12240590	0.95[CEU][hapmap];0.84[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs1253394	0.85[AMR][1000 genomes]
rs1253404	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1253427	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13439	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1468069	0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs1687369	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1687372	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2297987	0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs2484880	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2484881	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34787876	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61861820	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs701810	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs701812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs701813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs701815	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs701816	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs701817	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs701819	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs701821	0.85[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs7915926	0.85[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap]
rs793515	0.90[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs793516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793518	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs793519	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs793520	0.95[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs793524	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap]
rs946981	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1041614	chr10:98928281-99083056	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3361060	chr10:98939103-99025202	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1045553	chr10:98944397-99122203	Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv540750	chr10:98944397-99122203	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv433513	chr10:98970664-98976923	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs701814	RRP12	cis	parietal	SCAN
rs701814	TLX1	cis	cerebellum	SCAN
rs701814	EXOSC1	cis	parietal	SCAN
rs701814	FRAT1	cis	multi-tissue	Pritchard
rs701814	KIAA0690	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98956600-98976000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr10:98968000-98977600	Weak transcription	GM12878-XiMat	blood
3	chr10:98968000-98979000	Weak transcription	Fetal Thymus	thymus
4	chr10:98968000-98982200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr10:98968000-98982600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr10:98968200-98980600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr10:98970400-98982000	Weak transcription	Fetal Kidney	kidney
8	chr10:98970800-98982200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr10:98971200-98981400	Weak transcription	Fetal Muscle Leg	muscle
10	chr10:98971800-98982400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr10:98972400-98988400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr10:98973200-98981400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr10:98973400-98980200	Weak transcription	Fetal Intestine Small	intestine
14	chr10:98973400-98981400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr10:98973800-98979600	Weak transcription	Thymus	Thymus
16	chr10:98973800-99019000	Weak transcription	HepG2	liver
17	chr10:98974000-98982600	Weak transcription	Esophagus	oesophagus
18	chr10:98974000-98986200	Weak transcription	Pancreas	Pancrea
19	chr10:98974600-98977800	Weak transcription	Primary B cells from cord blood	blood
20	chr10:98975200-98981400	Weak transcription	Spleen	Spleen
21	chr10:98975400-98981000	Weak transcription	Fetal Stomach	stomach
22	chr10:98975600-98981800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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