Variant report

Variant	rs11162401
Chromosome Location	chr1:78419569-78419570
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	chr1:78419417-78421875	K562	blood:	n/a	n/a
2	POLR2A	chr1:78419556-78419920	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr1:78419522-78419962	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:78419137-78428700	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:78419518-78419921	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:78419557-78419850	GM12891	blood:	n/a	n/a
7	POLR2A	chr1:78419449-78419990	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:78419548-78419942	GM12891	blood:	n/a	n/a
9	POLR2A	chr1:78419532-78420038	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:78419539-78419876	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78416931..78420284-chr1:78442371..78445567,3	MCF-7	breast:

Variant related genes	Relation type
FUBP1	TF binding region
ENSG00000137960	Chromatin interaction
ENSG00000162616	Chromatin interaction
ENSG00000162613	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1039863	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10873961	0.86[ASN][1000 genomes]
rs10873962	0.81[ASN][1000 genomes]
rs10873963	0.81[ASN][1000 genomes]
rs1166696	0.93[ASN][1000 genomes]
rs1166699	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1166700	0.93[ASN][1000 genomes]
rs11805942	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11811805	0.99[ASN][1000 genomes]
rs1510244	0.86[ASN][1000 genomes]
rs17101101	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1749911	0.91[ASN][1000 genomes]
rs1749913	0.93[ASN][1000 genomes]
rs1780044	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1780045	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1780047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1780048	0.93[ASN][1000 genomes]
rs1780052	0.82[ASN][1000 genomes]
rs2296452	1.00[ASN][1000 genomes]
rs2296454	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736909	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767024	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767025	1.00[ASN][1000 genomes]
rs4083559	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4107671	0.86[ASN][1000 genomes]
rs4483454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4543852	0.86[ASN][1000 genomes]
rs60234511	0.89[AMR][1000 genomes]
rs6424648	0.91[ASN][1000 genomes]
rs6424653	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6680447	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6699513	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6702465	0.91[ASN][1000 genomes]
rs72685363	1.00[ASN][1000 genomes]
rs72685364	0.97[ASN][1000 genomes]
rs72685368	0.98[ASN][1000 genomes]
rs7520255	0.92[ASN][1000 genomes]
rs7524504	0.86[ASN][1000 genomes]
rs9661687	0.92[ASN][1000 genomes]
rs9662129	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9729146	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv518855	chr1:78416669-78456355	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78392200-78420400	Strong transcription	HSMM	muscle
2	chr1:78396800-78419600	Weak transcription	Ovary	ovary
3	chr1:78405800-78432200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:78405800-78442200	Strong transcription	Fetal Thymus	thymus
5	chr1:78406000-78420200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:78406000-78426600	Weak transcription	Fetal Heart	heart
7	chr1:78406000-78436200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:78406600-78436200	Strong transcription	Liver	Liver
9	chr1:78406600-78440600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:78406800-78436400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:78407000-78434400	Strong transcription	Dnd41	blood
12	chr1:78407000-78437200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:78407400-78427600	Strong transcription	Fetal Intestine Large	intestine
14	chr1:78407400-78432800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:78407400-78436600	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr1:78407400-78437600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:78407400-78437800	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr1:78407600-78435400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:78407600-78435600	Strong transcription	Duodenum Mucosa	Duodenum
20	chr1:78407600-78437200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:78407800-78420400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:78407800-78435400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:78407800-78436800	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr1:78407800-78437200	Strong transcription	Placenta	Placenta
25	chr1:78408000-78437600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:78408200-78434200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:78408400-78436400	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:78408400-78439600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:78408600-78437000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:78409600-78432000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:78409600-78432200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:78409600-78437200	Strong transcription	Hela-S3	cervix
33	chr1:78410000-78433800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:78410600-78427400	Strong transcription	HepG2	liver
35	chr1:78411400-78420800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr1:78411800-78421000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:78411800-78438200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:78412400-78434800	Strong transcription	Fetal Lung	lung
39	chr1:78412800-78434800	Strong transcription	Fetal Brain Female	brain
40	chr1:78413000-78423000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:78413000-78432600	Strong transcription	Primary T cells from cord blood	blood
42	chr1:78413400-78419600	Weak transcription	Brain Angular Gyrus	brain
43	chr1:78413800-78419600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:78413800-78420400	Weak transcription	Psoas Muscle	Psoas
45	chr1:78415000-78420200	Strong transcription	Osteobl	bone
46	chr1:78415000-78434200	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:78415000-78435800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:78415000-78437200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:78415200-78420000	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr1:78415200-78427200	Strong transcription	NH-A	brain

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