Variant report

Variant	rs9843340
Chromosome Location	chr3:156317073-156317074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156311042..156314506-chr3:156315758..156317660,4	K562	blood:
2	chr3:156316378..156327816-chr3:156388248..156396556,24	K562	blood:

Variant related genes	Relation type
ENSG00000243926	Chromatin interaction
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11718663	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12696038	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12696039	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13063385	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13063568	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13063746	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13090418	0.86[CEU][hapmap]
rs13092740	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13096478	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13314546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13317303	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13322475	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1401379	0.88[AMR][1000 genomes]
rs1510274	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16826570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16826572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17367831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1983205	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1995875	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2089735	0.86[CEU][hapmap]
rs2320894	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2320895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34016978	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34581312	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34667319	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35907778	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62285116	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6441080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6441081	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6650896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6762762	0.86[CEU][hapmap]
rs6808027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71310482	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7610493	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615297	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7615384	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7618375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7620297	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7633365	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7640363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7652356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs874641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs874642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs874662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs874663	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9289970	0.97[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs931989	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9631440	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812232	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9819659	0.85[CEU][hapmap]
rs9826775	0.92[CEU][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes]
rs9831507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9832367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9840361	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9840524	0.82[ASN][1000 genomes]
rs9840533	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9865431	0.93[CEU][hapmap]
rs9869703	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870053	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9870256	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9870575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9882596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]

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	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer 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	40 gene(s)	inside rSNPs	diseases
2	nsv829764	chr3:156174824-156347774	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	nsv877684	chr3:156294987-156344825	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9843340	OTOL1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156312000-156323000	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:156312200-156317200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:156312200-156317200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:156312200-156317200	Weak transcription	Left Ventricle	heart
5	chr3:156312600-156317400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:156312600-156323000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:156312800-156323400	Weak transcription	Brain Substantia Nigra	brain
8	chr3:156313000-156319400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:156315600-156317600	Enhancers	Fetal Intestine Large	intestine
10	chr3:156315800-156317600	Enhancers	Fetal Intestine Small	intestine
11	chr3:156316000-156317200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:156316000-156323600	Weak transcription	Brain Germinal Matrix	brain
13	chr3:156316400-156317600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr3:156316400-156319400	Enhancers	K562	blood
15	chr3:156316600-156317400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:156316600-156323400	Weak transcription	Ovary	ovary
17	chr3:156317000-156317200	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr3:156317000-156317400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:156317000-156317400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:156317000-156317600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:156317000-156317600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:156317000-156317600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:156317000-156317600	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr3:156317000-156317600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:156317000-156317600	Enhancers	Fetal Heart	heart

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