Variant report

Variant	rs62412528
Chromosome Location	chr6:56558385-56558386
allele	A/G
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	chr6:56557732-56558394	U87	brain:	n/a	n/a
2	FOS	chr6:56557995-56558477	MCF10A-Er-Src	breast:	n/a	chr6:56558019-56558031
3	TEAD4	chr6:56557828-56558582	HepG2	liver:	n/a	n/a
4	TCF12	chr6:56557331-56558452	A549	lung:	n/a	n/a
5	TBP	chr6:56557379-56558414	HepG2	liver:	n/a	n/a
6	FOXA1	chr6:56558024-56558467	HepG2	liver:	n/a	chr6:56558195-56558207
7	SP1	chr6:56557876-56558392	A549	lung:	n/a	n/a
8	NFIC	chr6:56557954-56558519	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:56556704-56558392	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:56557861-56558413	U87	brain:	n/a	n/a
11	CEBPB	chr6:56557978-56558385	IMR90	lung:	n/a	chr6:56557983-56557996
12	POLR2A	chr6:56557193-56558400	U87	brain:	n/a	n/a
13	CEBPB	chr6:56557171-56558399	Hela-S3	cervix:	n/a	chr6:56557983-56557996 chr6:56557482-56557495
14	FOXA2	chr6:56558015-56558500	HepG2	liver:	n/a	chr6:56558195-56558207
15	ARID3A	chr6:56557960-56558496	HepG2	liver:	n/a	n/a
16	EP300	chr6:56557858-56558529	HepG2	liver:	n/a	chr6:56558381-56558391 chr6:56558222-56558230
17	FOXA1	chr6:56557940-56558533	HepG2	liver:	n/a	chr6:56558195-56558207
18	POLR2A	chr6:56557861-56558417	U87	brain:	n/a	n/a
19	EP300	chr6:56557300-56558422	Hela-S3	cervix:	n/a	chr6:56558381-56558391 chr6:56558222-56558230 chr6:56557540-56557554 chr6:56557472-56557486
20	FOS	chr6:56557995-56558395	MCF10A-Er-Src	breast:	n/a	chr6:56558019-56558031

Variant related genes	Relation type
DST	TF binding region

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10498811	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11961141	0.83[EUR][1000 genomes]
rs11961342	0.85[EUR][1000 genomes]
rs11968575	0.83[EUR][1000 genomes]
rs13191164	1.00[EUR][1000 genomes]
rs13192037	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13192478	0.83[EUR][1000 genomes]
rs13192567	0.83[EUR][1000 genomes]
rs13196211	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13198399	0.83[EUR][1000 genomes]
rs13198938	0.83[EUR][1000 genomes]
rs13203000	0.83[EUR][1000 genomes]
rs13205013	1.00[EUR][1000 genomes]
rs13206849	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13210876	0.83[EUR][1000 genomes]
rs13213878	0.83[EUR][1000 genomes]
rs13217390	0.83[EUR][1000 genomes]
rs13219546	0.83[EUR][1000 genomes]
rs13219942	0.85[EUR][1000 genomes]
rs16888118	1.00[EUR][1000 genomes]
rs16888124	1.00[EUR][1000 genomes]
rs16888126	0.97[EUR][1000 genomes]
rs16888128	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16888130	0.98[EUR][1000 genomes]
rs16888133	0.97[EUR][1000 genomes]
rs16888135	0.83[EUR][1000 genomes]
rs17684511	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17684553	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17684571	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17751682	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17751695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2967960	0.82[EUR][1000 genomes]
rs2967963	0.81[EUR][1000 genomes]
rs3002003	0.83[EUR][1000 genomes]
rs3002004	0.83[EUR][1000 genomes]
rs3002006	0.83[EUR][1000 genomes]
rs3002007	0.81[EUR][1000 genomes]
rs3002008	0.83[EUR][1000 genomes]
rs3002009	0.83[EUR][1000 genomes]
rs3002010	0.83[EUR][1000 genomes]
rs3002011	0.83[EUR][1000 genomes]
rs34138864	1.00[EUR][1000 genomes]
rs34429594	0.84[EUR][1000 genomes]
rs34455199	0.83[EUR][1000 genomes]
rs34465210	0.83[EUR][1000 genomes]
rs34566275	0.83[EUR][1000 genomes]
rs34576803	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34587484	0.83[EUR][1000 genomes]
rs34623351	0.83[EUR][1000 genomes]
rs34724718	1.00[EUR][1000 genomes]
rs34803237	0.83[EUR][1000 genomes]
rs34812826	0.83[EUR][1000 genomes]
rs34824960	0.83[EUR][1000 genomes]
rs34832779	0.82[EUR][1000 genomes]
rs35206656	0.98[EUR][1000 genomes]
rs35326806	0.85[EUR][1000 genomes]
rs35408048	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35494794	0.85[EUR][1000 genomes]
rs35619924	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35637749	1.00[EUR][1000 genomes]
rs35668437	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35687635	0.98[EUR][1000 genomes]
rs35876418	0.83[EUR][1000 genomes]
rs35920751	0.83[EUR][1000 genomes]
rs36068365	0.85[EUR][1000 genomes]
rs4072271	0.98[EUR][1000 genomes]
rs4073960	0.95[EUR][1000 genomes]
rs4074101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4074102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4074103	0.97[EUR][1000 genomes]
rs41267675	0.83[EUR][1000 genomes]
rs4262190	0.91[EUR][1000 genomes]
rs4275049	0.83[EUR][1000 genomes]
rs4640889	0.83[EUR][1000 genomes]
rs5024547	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55742092	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56101897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59085778	0.83[EUR][1000 genomes]
rs59247267	0.83[EUR][1000 genomes]
rs60498201	0.83[EUR][1000 genomes]
rs62412526	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412532	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412556	0.83[EUR][1000 genomes]
rs6901176	1.00[EUR][1000 genomes]
rs6924375	1.00[EUR][1000 genomes]
rs6926134	0.83[EUR][1000 genomes]
rs6938003	0.82[EUR][1000 genomes]
rs71564848	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71564849	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7767128	1.00[EUR][1000 genomes]

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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv432888	chr6:56507489-56560764	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56543000-56559400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:56546200-56564800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:56547400-56561600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:56549600-56573600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr6:56549800-56578000	Weak transcription	Gastric	stomach
6	chr6:56553200-56558600	Active TSS	Fetal Intestine Large	intestine
7	chr6:56553200-56558600	Active TSS	Fetal Intestine Small	intestine
8	chr6:56553400-56558400	Active TSS	Right Ventricle	heart
9	chr6:56553600-56558400	Active TSS	Colonic Mucosa	Colon
10	chr6:56553600-56558400	Active TSS	Stomach Smooth Muscle	stomach
11	chr6:56553800-56558400	Active TSS	Right Atrium	heart
12	chr6:56553800-56560000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:56554000-56558400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:56554000-56560600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:56554000-56574600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:56554400-56558400	Active TSS	Psoas Muscle	Psoas
17	chr6:56554400-56558400	Flanking Active TSS	HepG2	liver
18	chr6:56554600-56558600	Flanking Active TSS	Osteobl	bone
19	chr6:56555000-56558400	Active TSS	Brain Cingulate Gyrus	brain
20	chr6:56555000-56558400	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr6:56555000-56558600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:56555200-56558400	Active TSS	Brain Angular Gyrus	brain
23	chr6:56555200-56558600	Enhancers	Fetal Heart	heart
24	chr6:56555400-56558400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:56555400-56558400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:56555400-56558400	Active TSS	Fetal Lung	lung
27	chr6:56555400-56558600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:56555400-56559400	Weak transcription	GM12878-XiMat	blood
29	chr6:56555400-56574600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:56555600-56558400	Active TSS	Colon Smooth Muscle	Colon
31	chr6:56555600-56559400	Weak transcription	Small Intestine	intestine
32	chr6:56555800-56558400	Active TSS	Duodenum Mucosa	Duodenum
33	chr6:56555800-56561200	Enhancers	HUVEC	blood vessel
34	chr6:56555800-56561800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:56555800-56573600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr6:56556000-56568400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr6:56556200-56573600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr6:56556200-56574400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:56556400-56561800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:56556400-56568000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:56556600-56558400	Flanking Active TSS	Hela-S3	cervix
42	chr6:56556600-56558400	Flanking Active TSS	NH-A	brain
43	chr6:56557000-56558400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:56557200-56558400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr6:56557200-56558600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr6:56557600-56558400	Flanking Active TSS	HSMMtube	muscle
47	chr6:56557600-56558400	Flanking Active TSS	NHDF-Ad	bronchial
48	chr6:56557600-56558600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:56557600-56558600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr6:56557600-56558800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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