Variant report

Variant	rs2297987
Chromosome Location	chr10:98989454-98989455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10736115	0.86[CEU][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs10748691	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10748694	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs10786319	0.92[ASN][1000 genomes]
rs10786321	0.86[CEU][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs10786327	0.95[CEU][hapmap];0.80[JPT][hapmap]
rs10786330	0.95[CEU][hapmap];0.80[JPT][hapmap]
rs10882880	0.94[ASN][1000 genomes]
rs10882881	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10882883	0.95[CEU][hapmap]
rs10882884	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs10882889	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap]
rs10882891	0.95[CEU][hapmap];0.85[JPT][hapmap]
rs11189037	0.90[ASN][1000 genomes]
rs11189038	0.90[ASN][1000 genomes]
rs11189052	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11189058	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189132	0.91[CEU][hapmap];0.80[JPT][hapmap]
rs1147600	0.89[EUR][1000 genomes]
rs12220695	0.96[ASN][1000 genomes]
rs12357266	0.93[ASN][1000 genomes]
rs1253427	0.81[EUR][1000 genomes]
rs13439	0.87[TSI][hapmap]
rs1468069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1687369	0.88[EUR][1000 genomes]
rs1687372	0.84[EUR][1000 genomes]
rs2009466	0.88[AMR][1000 genomes]
rs2065861	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2484880	0.82[EUR][1000 genomes]
rs2484881	0.82[EUR][1000 genomes]
rs2861875	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34787876	0.82[EUR][1000 genomes]
rs3740512	0.91[CEU][hapmap];0.80[JPT][hapmap]
rs3740522	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs3781373	0.82[CEU][hapmap]
rs3814164	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4917762	0.96[ASN][1000 genomes]
rs4917766	0.91[CEU][hapmap]
rs4919087	0.95[CEU][hapmap];0.80[JPT][hapmap]
rs701810	0.88[EUR][1000 genomes]
rs701812	0.88[EUR][1000 genomes]
rs701813	0.88[EUR][1000 genomes]
rs701814	0.88[EUR][1000 genomes]
rs701815	0.89[EUR][1000 genomes]
rs701816	0.88[EUR][1000 genomes]
rs701817	0.89[EUR][1000 genomes]
rs701819	0.89[EUR][1000 genomes]
rs701821	0.80[TSI][hapmap]
rs7078288	0.91[CEU][hapmap];0.80[JPT][hapmap]
rs7915926	0.80[TSI][hapmap]
rs793515	0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs793516	0.89[EUR][1000 genomes]
rs793517	0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs793518	0.81[EUR][1000 genomes]
rs793520	0.84[TSI][hapmap]
rs793524	0.87[TSI][hapmap]
rs8181326	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs945189	0.91[CEU][hapmap]
rs946981	0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs953097	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv1797410	chr10:98983785-99041740	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1040903	chr10:98986382-99047475	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2297987	KIAA0690	cis	multi-tissue	Pritchard
rs2297987	EXOSC1	cis	parietal	SCAN
rs2297987	FRAT1	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98973800-99019000	Weak transcription	HepG2	liver
2	chr10:98976000-99011400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr10:98977200-99023800	Weak transcription	Colonic Mucosa	Colon
4	chr10:98977400-99027000	Weak transcription	Right Ventricle	heart
5	chr10:98978200-99003400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr10:98978200-99003600	Weak transcription	NHEK	skin
7	chr10:98978600-99019000	Weak transcription	HSMMtube	muscle
8	chr10:98978600-99030400	Weak transcription	NH-A	brain
9	chr10:98978600-99037400	Weak transcription	HSMM	muscle
10	chr10:98978600-99051800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr10:98979000-98990400	Strong transcription	Fetal Thymus	thymus
12	chr10:98979000-99027400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr10:98979400-98989600	Weak transcription	NHLF	lung
14	chr10:98979400-99000600	Strong transcription	Dnd41	blood
15	chr10:98979600-98990000	Strong transcription	Thymus	Thymus
16	chr10:98979600-99003400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr10:98980200-98989600	Strong transcription	Primary T cells from cord blood	blood
18	chr10:98980200-98992800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr10:98980600-98990400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr10:98981000-99018200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr10:98981400-98989600	Strong transcription	Primary hematopoietic stem cells	blood
22	chr10:98981400-98990400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr10:98981400-99025400	Weak transcription	Colon Smooth Muscle	Colon
24	chr10:98982200-98990000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr10:98982200-98990200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr10:98982200-98991600	Strong transcription	Primary B cells from cord blood	blood
27	chr10:98982400-98998800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr10:98982400-99003400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr10:98982600-98992000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr10:98982600-98993200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr10:98982600-99007600	Weak transcription	Fetal Brain Female	brain
32	chr10:98982600-99007600	Weak transcription	Placenta	Placenta
33	chr10:98982600-99020800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr10:98982800-98999200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr10:98983000-98994200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr10:98983000-99003400	Weak transcription	Brain Anterior Caudate	brain
37	chr10:98983000-99022000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr10:98983000-99027200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr10:98983000-99027400	Weak transcription	Psoas Muscle	Psoas
40	chr10:98983000-99037600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr10:98983200-98990200	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr10:98983200-98994600	Weak transcription	Ovary	ovary
43	chr10:98983200-99027400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr10:98983800-98992600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr10:98984400-98989600	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr10:98984400-98990200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr10:98984400-98991800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr10:98984400-98992800	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr10:98984400-98993400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr10:98984600-98993000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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