Variant report

Variant	rs4926441
Chromosome Location	chr1:246933015-246933016
allele	A/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	chr1:246932605-246933022	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:246932603-246933036	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr1:246932573-246933041	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr1:246932575-246933040	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr1:246932564-246933032	MCF10A-Er-Src	breast:	n/a	n/a
6	RPC155	chr1:246932695-246933260	Hela-S3	cervix:	n/a	n/a
7	MYC	chr1:246932585-246933067	MCF10A-Er-Src	breast:	n/a	n/a
8	RCOR1	chr1:246932043-246933203	IMR90	lung:	n/a	n/a
9	STAT3	chr1:246932582-246933033	MCF10A-Er-Src	breast:	n/a	n/a
10	MXI1	chr1:246932432-246933120	SK-N-SH	brain:	n/a	n/a
11	MYC	chr1:246932577-246933066	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr1:246932522-246933032	U87	brain:	n/a	n/a
13	MXI1	chr1:246932460-246933139	IMR90	lung:	n/a	n/a
14	FOS	chr1:246932561-246933066	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246932646..246935152-chr1:246979853..246982699,2	K562	blood:

Variant related genes	Relation type
ENSG00000260855	TF binding region
ENSG00000235386	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10127783	0.86[EUR][1000 genomes]
rs10159002	0.86[EUR][1000 genomes]
rs10802442	0.86[EUR][1000 genomes]
rs10924820	0.86[EUR][1000 genomes]
rs10924823	0.86[EUR][1000 genomes]
rs10924824	0.86[EUR][1000 genomes]
rs12049149	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12058428	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12080111	0.81[AMR][1000 genomes]
rs12085823	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12090470	0.85[EUR][1000 genomes]
rs12135184	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12144408	0.86[EUR][1000 genomes]
rs34649985	0.86[EUR][1000 genomes]
rs34989088	0.85[EUR][1000 genomes]
rs3795462	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795463	0.86[EUR][1000 genomes]
rs3795465	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3935011	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4130316	0.85[EUR][1000 genomes]
rs4244627	0.86[EUR][1000 genomes]
rs4244628	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4244630	0.85[EUR][1000 genomes]
rs4926448	0.99[ASN][1000 genomes]
rs4926451	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4926453	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4926454	0.86[EUR][1000 genomes]
rs4926455	0.85[EUR][1000 genomes]
rs4926457	0.86[EUR][1000 genomes]
rs6426328	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6426331	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6426332	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426334	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6664091	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6664883	0.86[EUR][1000 genomes]
rs6686584	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7513803	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7537149	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7549965	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7556120	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9426267	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv873423	chr1:246923861-246978504	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
2	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:246895000-246942200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:246895400-246938600	Weak transcription	Fetal Heart	heart
5	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:246904600-246942800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:246905000-246945800	Weak transcription	Psoas Muscle	Psoas
8	chr1:246912800-246933200	Weak transcription	K562	blood
9	chr1:246917600-246936000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:246920800-246944200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:246921200-246943200	Strong transcription	Dnd41	blood
12	chr1:246921600-246945800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:246922000-246936400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:246922200-246934400	Strong transcription	Placenta	Placenta
15	chr1:246922200-246936000	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr1:246922200-246936000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:246922200-246936200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:246922200-246937000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:246922200-246944600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr1:246922600-246936400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:246923000-246936200	Strong transcription	Primary hematopoietic stem cells	blood
22	chr1:246923200-246945000	Strong transcription	Fetal Muscle Leg	muscle
23	chr1:246923600-246933200	Strong transcription	Brain Hippocampus Middle	brain
24	chr1:246924000-246941200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:246924000-246944200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:246924400-246934600	Weak transcription	Fetal Brain Male	brain
27	chr1:246924400-246939200	Weak transcription	Colonic Mucosa	Colon
28	chr1:246924400-246945800	Weak transcription	Primary B cells from cord blood	blood
29	chr1:246925200-246952200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:246925400-246936600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:246926400-246939200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:246928200-246933600	Weak transcription	Fetal Kidney	kidney
33	chr1:246928200-246934600	Weak transcription	A549	lung
34	chr1:246928600-246937000	Strong transcription	Fetal Stomach	stomach
35	chr1:246928800-246934000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:246928800-246944800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:246929200-246936800	Strong transcription	Fetal Brain Female	brain
38	chr1:246930600-246939000	Weak transcription	Thymus	Thymus
39	chr1:246931000-246934800	Weak transcription	Fetal Lung	lung
40	chr1:246931000-246936800	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr1:246931200-246933600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:246931200-246937800	Weak transcription	NH-A	brain
43	chr1:246931200-246940600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:246932000-246933600	Genic enhancers	Muscle Satellite Cultured Cells	--
45	chr1:246932000-246936600	Weak transcription	Aorta	Aorta
46	chr1:246932000-246939200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:246932200-246933200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:246932200-246933200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:246932200-246934800	Weak transcription	HSMMtube	muscle
50	chr1:246932200-246935000	Weak transcription	GM12878-XiMat	blood

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