Variant report

Variant	rs10420465
Chromosome Location	chr19:44665977-44665978
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:44665783-44666056	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr19:44665783-44666132	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:44665844-44666027	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44659490..44662168-chr19:44665073..44667043,2	MCF-7	breast:
2	chr19:44664505..44666097-chr19:44668997..44671090,2	K562	blood:
3	chr19:44648468..44650180-chr19:44664736..44666479,2	K562	blood:

Variant related genes	Relation type
ZNF226	TF binding region
ENSG00000167380	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10153465	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10153499	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10405281	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10406980	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10408004	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409884	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409954	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10410283	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412910	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10415563	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs10415664	0.88[ASN][1000 genomes]
rs10416230	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416292	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10417178	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10422555	0.96[ASN][1000 genomes]
rs10422609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10424371	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10425146	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10425881	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10426314	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1106562	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11140	0.90[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11878679	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11878720	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11879588	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11879843	0.90[ASN][1000 genomes]
rs13346417	0.82[ASN][1000 genomes]
rs16959114	0.85[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs16978665	0.83[JPT][hapmap]
rs16978738	0.85[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs16978794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16978836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1881748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141524	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141525	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2178342	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28422007	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3746322	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs3803932	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3810137	0.92[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4802212	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802213	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802215	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4803683	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4803685	1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4803686	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4803688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4803692	0.85[CHB][hapmap];0.91[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4803693	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55732275	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57418162	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57451052	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58358390	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59576456	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59774711	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60379253	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60747128	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509142	0.81[JPT][hapmap]
rs6509144	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6509147	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6509148	1.00[CHB][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248797	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250439	0.81[JPT][hapmap]
rs7254034	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254458	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7259777	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs7260367	1.00[CHB][hapmap];1.00[JPT][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]
rs7260588	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs73564059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73564095	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107252	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108504	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8108908	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111388	0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs8111562	0.83[JPT][hapmap]
rs922063	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs922064	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9304639	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44647800-44668400	ZNF genes & repeats	Liver	Liver
2	chr19:44652400-44667600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:44653800-44668200	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr19:44661400-44668600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:44661600-44668200	Weak transcription	HepG2	liver
6	chr19:44662200-44668400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr19:44662200-44668400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr19:44662200-44668400	Weak transcription	Fetal Heart	heart
9	chr19:44662200-44668600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:44662200-44668600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr19:44662200-44668600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:44662200-44668600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr19:44662200-44668600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:44662200-44668600	Weak transcription	Fetal Brain Female	brain
15	chr19:44662200-44668600	Weak transcription	Right Ventricle	heart
16	chr19:44662200-44668600	Weak transcription	NHDF-Ad	bronchial
17	chr19:44662200-44668800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:44662400-44668400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:44662400-44668400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:44662400-44668600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:44662600-44669000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:44662800-44668600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:44663200-44668400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:44663400-44668400	Weak transcription	Brain Germinal Matrix	brain
25	chr19:44663400-44668600	Weak transcription	Osteobl	bone
26	chr19:44663600-44668400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr19:44665800-44668800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

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