Variant report

Variant	rs41302545
Chromosome Location	chr1:154525999-154526000
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	FOS	chr1:154525854-154526289	MCF10A-Er-Src	breast:	n/a	chr1:154526023-154526031
2	E2F4	chr1:154525907-154526180	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:154525787-154526124	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:154525574-154526144	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:154525603-154526352	GM12892	blood:	n/a	n/a
6	STAT3	chr1:154525827-154526221	MCF10A-Er-Src	breast:	n/a	chr1:154525990-154526001
7	NFIC	chr1:154525452-154526053	ECC-1	luminal epithelium:	n/a	chr1:154525732-154525749 chr1:154525734-154525750
8	STAT3	chr1:154525886-154526200	MCF10A-Er-Src	breast:	n/a	chr1:154525990-154526001
9	STAT3	chr1:154525592-154526313	MCF10A-Er-Src	breast:	n/a	chr1:154525990-154526001
10	POLR2A	chr1:154525808-154526008	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:154525895-154526586	PFSK-1	brain:	n/a	n/a
12	NFIC	chr1:154525476-154526101	ECC-1	luminal epithelium:	n/a	chr1:154525732-154525749 chr1:154525734-154525750
13	FOS	chr1:154525884-154526256	MCF10A-Er-Src	breast:	n/a	chr1:154526023-154526031
14	FOS	chr1:154525872-154526288	MCF10A-Er-Src	breast:	n/a	chr1:154526023-154526031

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154450305..154454149-chr1:154524357..154527096,3	MCF-7	breast:

Variant related genes	Relation type
UBE2Q1	TF binding region
UBE2Q1-AS1	TF binding region
ENSG00000273110	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10159236	0.85[EUR][1000 genomes]
rs10752642	0.95[EUR][1000 genomes]
rs10752643	0.97[EUR][1000 genomes]
rs10908844	0.97[EUR][1000 genomes]
rs10908846	0.97[EUR][1000 genomes]
rs11265627	0.94[EUR][1000 genomes]
rs11265629	0.89[EUR][1000 genomes]
rs11265634	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11804305	0.82[EUR][1000 genomes]
rs12118074	0.95[EUR][1000 genomes]
rs12124333	0.95[EUR][1000 genomes]
rs14021	0.94[EUR][1000 genomes]
rs16836054	0.96[EUR][1000 genomes]
rs4074436	0.91[ASN][1000 genomes]
rs4131514	0.97[EUR][1000 genomes]
rs4269769	0.97[EUR][1000 genomes]
rs4288587	0.97[EUR][1000 genomes]
rs4307559	0.92[EUR][1000 genomes]
rs4307560	0.80[EUR][1000 genomes]
rs4308966	0.85[EUR][1000 genomes]
rs4329505	0.85[EUR][1000 genomes]
rs4345796	0.83[EUR][1000 genomes]
rs4474240	0.95[EUR][1000 genomes]
rs4518898	0.97[EUR][1000 genomes]
rs4575077	0.97[EUR][1000 genomes]
rs4585969	0.97[EUR][1000 genomes]
rs4845634	0.96[EUR][1000 genomes]
rs4845635	0.95[EUR][1000 genomes]
rs4845636	0.95[EUR][1000 genomes]
rs4845640	0.97[EUR][1000 genomes]
rs4845641	0.97[EUR][1000 genomes]
rs4845643	0.91[EUR][1000 genomes]
rs4845644	0.98[EUR][1000 genomes]
rs4845648	0.98[EUR][1000 genomes]
rs56047170	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56233546	0.96[EUR][1000 genomes]
rs61811362	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs61812599	0.81[EUR][1000 genomes]
rs61812626	0.83[EUR][1000 genomes]
rs61812631	0.96[EUR][1000 genomes]
rs61812654	0.98[EUR][1000 genomes]
rs6427716	0.97[EUR][1000 genomes]
rs6427720	0.92[EUR][1000 genomes]
rs6427721	0.81[EUR][1000 genomes]
rs6427722	0.97[EUR][1000 genomes]
rs6427724	0.92[EUR][1000 genomes]
rs6656395	0.97[EUR][1000 genomes]
rs6662503	0.94[EUR][1000 genomes]
rs6670375	0.97[EUR][1000 genomes]
rs6687112	0.97[EUR][1000 genomes]
rs6689710	0.88[EUR][1000 genomes]
rs6691727	0.97[EUR][1000 genomes]
rs6696177	0.90[EUR][1000 genomes]
rs6697103	0.97[EUR][1000 genomes]
rs6697115	0.97[EUR][1000 genomes]
rs6701586	0.97[EUR][1000 genomes]
rs6703672	0.87[EUR][1000 genomes]
rs72698167	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7513603	0.95[EUR][1000 genomes]
rs7526247	0.90[EUR][1000 genomes]
rs7539745	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543174	0.91[EUR][1000 genomes]
rs7550664	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7553602	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9427076	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9427082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9427415	1.00[AFR][1000 genomes];0.98[EUR][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	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 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	chr1:154513600-154528400	Weak transcription	Right Atrium	heart
2	chr1:154518000-154526000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:154520000-154528200	Strong transcription	Placenta	Placenta
4	chr1:154520600-154528400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:154520600-154528800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:154520600-154528800	Strong transcription	Primary T cells from cord blood	blood
7	chr1:154520800-154528400	Strong transcription	Adipose Nuclei	Adipose
8	chr1:154520800-154528400	Strong transcription	Placenta Amnion	Placenta Amnion
9	chr1:154520800-154528600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:154520800-154528800	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:154521000-154528200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:154521000-154528200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:154521000-154528600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:154521000-154528600	Strong transcription	Fetal Thymus	thymus
15	chr1:154521200-154526000	Strong transcription	Fetal Muscle Leg	muscle
16	chr1:154521200-154526200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:154521200-154526200	Strong transcription	NHEK	skin
18	chr1:154521200-154527800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:154521200-154528200	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr1:154521200-154528200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr1:154521200-154528400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:154521200-154528400	Strong transcription	Primary B cells from cord blood	blood
23	chr1:154521200-154528400	Strong transcription	Brain Anterior Caudate	brain
24	chr1:154521200-154528400	Strong transcription	Brain Hippocampus Middle	brain
25	chr1:154521200-154528400	Strong transcription	HUVEC	blood vessel
26	chr1:154521200-154528400	Strong transcription	NH-A	brain
27	chr1:154521200-154528600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:154521200-154528600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:154521200-154528600	Strong transcription	HSMM	muscle
30	chr1:154521200-154528800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:154521200-154528800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:154521200-154528800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:154521400-154527800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr1:154521400-154528000	Strong transcription	Brain Substantia Nigra	brain
35	chr1:154521400-154528200	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:154521400-154528200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:154521400-154528200	Strong transcription	Lung	lung
38	chr1:154521400-154528200	Strong transcription	Spleen	Spleen
39	chr1:154521400-154528200	Strong transcription	NHDF-Ad	bronchial
40	chr1:154521400-154528400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:154521400-154528400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:154521400-154528400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:154521400-154528400	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr1:154521400-154528600	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr1:154521400-154528600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:154521400-154528600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr1:154521400-154528800	Strong transcription	Thymus	Thymus
48	chr1:154521400-154529000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr1:154521600-154528200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:154521600-154528400	Strong transcription	ES-I3 Cell Line	embryonic stem cell

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