Variant report

Variant	rs1543376
Chromosome Location	chr6:128564206-128564207
allele	C/T
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	chr6:128564174-128564372	MCF10A-Er-Src	breast:	n/a	n/a
2	FOXA1	chr6:128563964-128564334	HepG2	liver:	n/a	chr6:128564276-128564288
3	FOXA1	chr6:128563917-128564263	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
PTPRK	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10485160	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11961542	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11962214	1.00[CEU][hapmap]
rs12055654	0.95[ASN][1000 genomes]
rs12055776	0.80[ASN][1000 genomes]
rs1339188	1.00[CEU][hapmap]
rs1538498	1.00[CEU][hapmap]
rs17055441	0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs17055450	1.00[CEU][hapmap]
rs17055452	1.00[CEU][hapmap]
rs17055472	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17055477	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17055628	1.00[CEU][hapmap]
rs17055630	1.00[CEU][hapmap]
rs17055679	1.00[CEU][hapmap]
rs1738283	1.00[CEU][hapmap]
rs1738288	1.00[CEU][hapmap]
rs1738290	1.00[CEU][hapmap]
rs1768347	1.00[CEU][hapmap]
rs1768353	1.00[CEU][hapmap]
rs1768357	1.00[CEU][hapmap]
rs2073161	0.89[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs2076572	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3813371	1.00[CEU][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3813372	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs3813373	1.00[CEU][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4140541	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4243494	0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs4421217	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4440487	1.00[CEU][hapmap]
rs4483000	0.89[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4897252	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61583694	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6913718	1.00[CEU][hapmap]
rs6928143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6933029	0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs6938118	1.00[CEU][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs730202	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73590673	0.95[ASN][1000 genomes]
rs742736	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7753945	0.84[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7754321	1.00[CEU][hapmap]
rs7755473	0.90[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs7755836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7772941	1.00[CEU][hapmap]
rs7773849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7776405	1.00[CEU][hapmap]
rs9321113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9372885	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9372886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9372887	0.89[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs9375550	1.00[CEU][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9375551	0.86[ASN][1000 genomes]
rs9375552	0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs9375554	0.88[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs9375555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[ASN][1000 genomes]
rs9375556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9375557	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9375558	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9385452	0.89[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs9385454	0.81[ASN][1000 genomes]
rs9385455	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9388618	0.84[ASN][1000 genomes]
rs9388619	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9388621	0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs9388622	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs9388624	0.89[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs9388625	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9388626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9388627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9398866	0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs9398867	0.89[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs9398868	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9402023	0.84[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9402024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9402025	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs9402027	0.90[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs9402028	0.80[ASN][1000 genomes]
rs9402029	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9402030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9402031	0.82[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs9402032	0.89[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9784773	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9784880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs981998	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv886651	chr6:128450019-128565778	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128488200-128565200	Weak transcription	Fetal Stomach	stomach
2	chr6:128492600-128567800	Weak transcription	Ovary	ovary
3	chr6:128520400-128573800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:128531200-128567800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:128531200-128573800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:128537600-128573800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:128540200-128564800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:128540400-128569400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:128551400-128565800	Weak transcription	Psoas Muscle	Psoas
10	chr6:128551400-128584400	Weak transcription	Pancreas	Pancrea
11	chr6:128553200-128573800	Weak transcription	NHLF	lung
12	chr6:128553400-128564400	Weak transcription	Lung	lung
13	chr6:128553800-128570600	Weak transcription	Liver	Liver
14	chr6:128555000-128564400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:128555200-128584400	Weak transcription	HMEC	breast
16	chr6:128555600-128595800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:128555800-128564800	Weak transcription	Fetal Brain Female	brain
18	chr6:128556600-128564400	Strong transcription	HepG2	liver
19	chr6:128559600-128570600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:128559800-128565600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:128561000-128564400	Strong transcription	NHEK	skin
22	chr6:128561400-128564800	Weak transcription	Osteobl	bone
23	chr6:128561400-128567800	Weak transcription	Right Ventricle	heart
24	chr6:128561400-128573000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr6:128561400-128587000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:128561600-128567600	Weak transcription	Brain Angular Gyrus	brain
27	chr6:128561600-128569200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:128561600-128573800	Weak transcription	Thymus	Thymus
29	chr6:128562400-128576600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:128562600-128567400	Weak transcription	Brain Anterior Caudate	brain
31	chr6:128562600-128573600	Weak transcription	Primary T cells from cord blood	blood
32	chr6:128562800-128564400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:128562800-128564400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:128562800-128567600	Weak transcription	Brain Substantia Nigra	brain
35	chr6:128562800-128567600	Weak transcription	Fetal Intestine Large	intestine
36	chr6:128562800-128567800	Weak transcription	Right Atrium	heart
37	chr6:128562800-128568000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:128562800-128573000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:128562800-128573000	Weak transcription	Aorta	Aorta
40	chr6:128562800-128573800	Weak transcription	Gastric	stomach
41	chr6:128562800-128579800	Weak transcription	Left Ventricle	heart
42	chr6:128562800-128588200	Weak transcription	HUVEC	blood vessel
43	chr6:128563000-128570600	Weak transcription	HSMMtube	muscle
44	chr6:128563000-128573000	Weak transcription	NH-A	brain
45	chr6:128563000-128574000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:128563000-128585400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:128563200-128567600	Weak transcription	Fetal Intestine Small	intestine
48	chr6:128563600-128564600	Strong transcription	Fetal Thymus	thymus
49	chr6:128563800-128566200	Weak transcription	HSMM	muscle
50	chr6:128563800-128567800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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