Variant report

Variant	rs4344199
Chromosome Location	chr9:99549449-99549450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 138 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10115492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10115621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10115814	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs10116146	1.00[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes]
rs10116439	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10116462	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs10116733	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10117162	0.88[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10117921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10117923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10118617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10118825	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10119439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119466	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10120515	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10121500	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10121639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10122464	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124033	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs10124911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10816533	1.00[CEU][hapmap];0.85[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs10816535	0.95[AMR][1000 genomes]
rs10816541	0.87[AMR][1000 genomes]
rs10816560	1.00[ASN][1000 genomes]
rs10816572	1.00[ASN][1000 genomes]
rs10816602	0.99[ASN][1000 genomes]
rs10816647	1.00[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes]
rs10816663	0.99[ASN][1000 genomes]
rs10978778	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10978862	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10978891	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs10978909	0.82[CHB][hapmap];0.87[JPT][hapmap];0.98[ASN][1000 genomes]
rs10978916	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10978917	0.98[ASN][1000 genomes]
rs10978952	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10978953	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10978963	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10978965	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10978968	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10978970	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10978971	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10979019	1.00[ASN][1000 genomes]
rs10979020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10979152	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10979175	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10979212	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs10979216	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10979224	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10979266	0.99[ASN][1000 genomes]
rs10979268	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10979329	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10979353	0.99[ASN][1000 genomes]
rs11534219	1.00[ASN][1000 genomes]
rs12004507	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12236125	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12236179	0.87[AMR][1000 genomes]
rs12237908	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12336500	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12339579	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12340602	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12347618	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs12349952	0.93[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12352138	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12352656	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327781	1.00[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes]
rs16911458	1.00[CEU][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap]
rs16911569	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2281952	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2289649	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2289651	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2486612	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs28489285	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28510174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28592903	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28667636	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28677792	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28678226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28786462	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28844439	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35334289	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35906155	1.00[AMR][1000 genomes]
rs3758298	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3758299	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3780549	1.00[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes]
rs3780550	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs3780551	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes]
rs3780552	1.00[CEU][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs3780553	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs3824482	1.00[AMR][1000 genomes]
rs41306482	0.95[ASN][1000 genomes]
rs4538990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4645656	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap]
rs57046479	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57364635	0.99[ASN][1000 genomes]
rs60072763	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60386249	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6477715	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7022992	0.99[ASN][1000 genomes]
rs7025027	0.95[EUR][1000 genomes]
rs7025321	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7030131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030521	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7032889	0.87[AMR][1000 genomes]
rs7036728	0.99[ASN][1000 genomes]
rs7037100	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7037169	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7041773	0.82[EUR][1000 genomes]
rs7044941	0.95[EUR][1000 genomes]
rs73546584	0.87[AMR][1000 genomes]
rs73552429	0.95[ASN][1000 genomes]
rs73654606	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73654610	0.99[ASN][1000 genomes]
rs7846956	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7847117	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7847558	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7847673	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7848081	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7848710	0.84[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs7850707	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7854468	0.95[EUR][1000 genomes]
rs7856667	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7858098	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7859307	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs7859940	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7860308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7860672	0.95[EUR][1000 genomes]
rs7860985	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7861923	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7864360	0.87[AMR][1000 genomes]
rs7870376	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7870734	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7874781	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430084	chr9:99383945-99551945	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1053215	chr9:99483926-99824810	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv831660	chr9:99485058-99672080	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv520001	chr9:99533434-99795125	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv6624	chr9:99548787-99593968	ZNF genes & repeats Weak transcription Strong transcription Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4344199	LOC642921	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99541200-99550200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:99541200-99550200	Weak transcription	Left Ventricle	heart
3	chr9:99541200-99550200	Weak transcription	HSMM	muscle
4	chr9:99541200-99550400	Weak transcription	Pancreas	Pancrea
5	chr9:99541200-99552000	Weak transcription	Psoas Muscle	Psoas
6	chr9:99541400-99551800	Weak transcription	Fetal Stomach	stomach
7	chr9:99541600-99550200	Weak transcription	Brain Angular Gyrus	brain
8	chr9:99541600-99550200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:99541600-99550400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr9:99541600-99551200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:99541600-99552200	Weak transcription	Fetal Lung	lung
12	chr9:99541800-99550400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr9:99541800-99556400	Weak transcription	Fetal Heart	heart
14	chr9:99542600-99553400	Weak transcription	Dnd41	blood
15	chr9:99547000-99550000	Weak transcription	Primary B cells from cord blood	blood
16	chr9:99547800-99551200	ZNF genes & repeats	Liver	Liver
17	chr9:99548000-99551200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:99548200-99550800	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr9:99548600-99550200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr9:99548600-99551200	Strong transcription	Brain Germinal Matrix	brain
21	chr9:99548800-99550000	Weak transcription	Ovary	ovary
22	chr9:99548800-99550800	Weak transcription	Brain Hippocampus Middle	brain
23	chr9:99548800-99557000	Weak transcription	Right Ventricle	heart
24	chr9:99549000-99550200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr9:99549000-99551800	Weak transcription	HSMMtube	muscle
26	chr9:99549400-99550800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood

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