Variant report

Variant	rs11963575
Chromosome Location	chr6:128843260-128843261
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:128843249-128843430	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:128529927..128532522-chr6:128841893..128843396,2	MCF-7	breast:
2	chr6:128669634..128671989-chr6:128842689..128844220,2	MCF-7	breast:
3	chr6:128666022..128668619-chr6:128842327..128844085,2	MCF-7	breast:
4	chr6:128843117..128845172-chr6:128863675..128865893,2	MCF-7	breast:
5	chr6:128819294..128822394-chr6:128840492..128843286,6	MCF-7	breast:
6	chr6:128817983..128822479-chr6:128839649..128843314,6	MCF-7	breast:

No data

Variant related genes	Relation type
PTPRK	TF binding region
ENSG00000224733	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10085245	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10085247	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10085248	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10223535	1.00[ASN][1000 genomes]
rs10872331	1.00[ASN][1000 genomes]
rs11154439	1.00[ASN][1000 genomes]
rs11154440	1.00[ASN][1000 genomes]
rs11751628	1.00[ASN][1000 genomes]
rs11752256	1.00[ASN][1000 genomes]
rs11753496	1.00[ASN][1000 genomes]
rs11758545	1.00[ASN][1000 genomes]
rs11758690	1.00[ASN][1000 genomes]
rs12524679	1.00[ASN][1000 genomes]
rs12525214	1.00[ASN][1000 genomes]
rs12526634	1.00[ASN][1000 genomes]
rs12526667	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527086	1.00[ASN][1000 genomes]
rs12527265	1.00[ASN][1000 genomes]
rs12529229	1.00[ASN][1000 genomes]
rs12529511	1.00[ASN][1000 genomes]
rs12529947	1.00[ASN][1000 genomes]
rs12529948	1.00[ASN][1000 genomes]
rs1341584	1.00[ASN][1000 genomes]
rs1341585	1.00[ASN][1000 genomes]
rs13437323	1.00[ASN][1000 genomes]
rs1361595	0.87[EUR][1000 genomes]
rs1572964	1.00[ASN][1000 genomes]
rs17055952	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17056043	1.00[ASN][1000 genomes]
rs17364020	1.00[ASN][1000 genomes]
rs17364090	1.00[ASN][1000 genomes]
rs17364118	1.00[ASN][1000 genomes]
rs17364153	1.00[ASN][1000 genomes]
rs17461370	1.00[ASN][1000 genomes]
rs17461759	1.00[ASN][1000 genomes]
rs1935131	1.00[ASN][1000 genomes]
rs2326702	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55988836	1.00[ASN][1000 genomes]
rs57922933	1.00[ASN][1000 genomes]
rs62425737	1.00[ASN][1000 genomes]
rs62425738	1.00[ASN][1000 genomes]
rs62425739	1.00[ASN][1000 genomes]
rs62425740	1.00[ASN][1000 genomes]
rs62425742	1.00[ASN][1000 genomes]
rs62425743	1.00[ASN][1000 genomes]
rs62425744	1.00[ASN][1000 genomes]
rs62426790	1.00[ASN][1000 genomes]
rs62426791	1.00[ASN][1000 genomes]
rs62426792	1.00[ASN][1000 genomes]
rs62426793	1.00[ASN][1000 genomes]
rs62426794	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426795	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62426796	1.00[ASN][1000 genomes]
rs62426797	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62426798	1.00[ASN][1000 genomes]
rs62426799	1.00[ASN][1000 genomes]
rs62426800	1.00[ASN][1000 genomes]
rs62426801	1.00[ASN][1000 genomes]
rs62426804	1.00[ASN][1000 genomes]
rs62426805	1.00[ASN][1000 genomes]
rs62426806	1.00[ASN][1000 genomes]
rs62426840	1.00[ASN][1000 genomes]
rs62426841	1.00[ASN][1000 genomes]
rs62426842	1.00[ASN][1000 genomes]
rs62426844	1.00[ASN][1000 genomes]
rs62426846	1.00[ASN][1000 genomes]
rs62426847	1.00[ASN][1000 genomes]
rs62426848	1.00[ASN][1000 genomes]
rs62426849	1.00[ASN][1000 genomes]
rs62426850	1.00[ASN][1000 genomes]
rs62426851	1.00[ASN][1000 genomes]
rs62426853	1.00[ASN][1000 genomes]
rs62427780	1.00[ASN][1000 genomes]
rs62427781	1.00[ASN][1000 genomes]
rs6569529	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6569533	0.86[EUR][1000 genomes]
rs6916193	0.85[EUR][1000 genomes]
rs6920943	0.85[EUR][1000 genomes]
rs6923822	0.84[EUR][1000 genomes]
rs6924111	0.91[EUR][1000 genomes]
rs6935611	0.86[EUR][1000 genomes]
rs714782	1.00[ASN][1000 genomes]
rs7356818	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7356912	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7454742	1.00[ASN][1000 genomes]
rs766306	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7738739	1.00[ASN][1000 genomes]
rs7739600	1.00[ASN][1000 genomes]
rs7745291	0.86[EUR][1000 genomes]
rs7748742	1.00[ASN][1000 genomes]
rs7751094	1.00[ASN][1000 genomes]
rs7752487	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760287	1.00[ASN][1000 genomes]
rs7760330	0.88[EUR][1000 genomes]
rs7760572	1.00[ASN][1000 genomes]
rs7760682	1.00[ASN][1000 genomes]
rs7765212	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768240	1.00[ASN][1000 genomes]
rs7771701	1.00[ASN][1000 genomes]
rs9321122	1.00[ASN][1000 genomes]
rs9372894	0.85[EUR][1000 genomes]
rs9375575	0.86[EUR][1000 genomes]
rs9388651	0.85[EUR][1000 genomes]
rs9388654	0.85[EUR][1000 genomes]
rs947358	0.84[EUR][1000 genomes]
rs9482892	1.00[ASN][1000 genomes]
rs9482893	1.00[ASN][1000 genomes]
rs9482897	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9482902	1.00[ASN][1000 genomes]
rs9482904	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9491988	1.00[ASN][1000 genomes]
rs9491990	0.91[EUR][1000 genomes]
rs9491997	0.85[EUR][1000 genomes]
rs9491999	0.85[EUR][1000 genomes]
rs9492000	1.00[ASN][1000 genomes]
rs9492001	0.85[EUR][1000 genomes]
rs9492002	1.00[ASN][1000 genomes]
rs9492004	1.00[ASN][1000 genomes]
rs9492005	1.00[ASN][1000 genomes]
rs9492008	1.00[ASN][1000 genomes]
rs9492011	1.00[ASN][1000 genomes]
rs9492013	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492014	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492017	1.00[ASN][1000 genomes]
rs9492018	1.00[ASN][1000 genomes]
rs9492020	1.00[ASN][1000 genomes]
rs9492021	1.00[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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2758078	chr6:128842192-128844831	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv2759468	chr6:128842192-128844831	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 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	chr6:128842400-128846200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:128842600-128845400	Weak transcription	Pancreas	Pancrea
3	chr6:128842600-128848800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:128842800-128843400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:128842800-128843400	Enhancers	Brain Cingulate Gyrus	brain
6	chr6:128842800-128843400	Enhancers	HSMM	muscle
7	chr6:128842800-128843400	Enhancers	NH-A	brain
8	chr6:128842800-128843800	Enhancers	HepG2	liver
9	chr6:128842800-128844000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:128842800-128844600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:128842800-128845600	Weak transcription	Fetal Heart	heart
12	chr6:128842800-128845800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:128842800-128846200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:128842800-128846200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:128842800-128846400	Weak transcription	Brain Hippocampus Middle	brain
16	chr6:128842800-128846400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr6:128842800-128846400	Weak transcription	Brain Substantia Nigra	brain
18	chr6:128842800-128846600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:128842800-128847000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:128842800-128853800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:128843000-128843400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:128843000-128843400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:128843000-128843400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr6:128843000-128845800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:128843000-128846400	Weak transcription	Fetal Brain Male	brain
26	chr6:128843000-128846400	Weak transcription	Fetal Brain Female	brain
27	chr6:128843200-128845600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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