Variant report

Variant	rs1012554
Chromosome Location	chr10:50739557-50739558
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	CEBPB	chr10:50739367-50739612	HepG2	liver:	n/a	chr10:50739486-50739497 chr10:50739488-50739497
2	CEBPB	chr10:50739359-50739647	IMR90	lung:	n/a	chr10:50739486-50739497 chr10:50739488-50739497

No.	Distal block	Cell Line	Cell type
1	chr10:50717195..50718876-chr10:50739121..50741065,2	K562	blood:
2	chr10:50737860..50742863-chr10:50744224..50749108,7	MCF-7	breast:
3	chr10:50738435..50741425-chr10:50746279..50748741,3	MCF-7	breast:

Variant related genes	Relation type
ERCC6	TF binding region
ENSG00000225830	Chromatin interaction
ENSG00000258838	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1012553	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776576	0.95[ASN][1000 genomes]
rs10776580	0.80[ASN][1000 genomes]
rs10857503	0.90[ASN][1000 genomes]
rs10857505	0.81[ASN][1000 genomes]
rs11101140	0.94[ASN][1000 genomes]
rs11101148	0.93[ASN][1000 genomes]
rs11101153	0.89[ASN][1000 genomes]
rs11101154	0.89[ASN][1000 genomes]
rs11527799	0.89[ASN][1000 genomes]
rs11594945	0.90[ASN][1000 genomes]
rs11815415	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12161717	0.80[ASN][1000 genomes]
rs12217467	0.89[ASN][1000 genomes]
rs12218455	0.90[ASN][1000 genomes]
rs12218602	0.89[ASN][1000 genomes]
rs12220258	0.91[ASN][1000 genomes]
rs12413113	0.82[ASN][1000 genomes]
rs17177703	0.81[ASN][1000 genomes]
rs17784189	0.80[ASN][1000 genomes]
rs1880679	0.81[ASN][1000 genomes]
rs1880680	0.81[ASN][1000 genomes]
rs1917799	0.90[ASN][1000 genomes]
rs1924488	0.95[ASN][1000 genomes]
rs2222638	0.81[ASN][1000 genomes]
rs2228524	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228528	0.99[ASN][1000 genomes]
rs2889771	0.89[ASN][1000 genomes]
rs3750745	0.90[ASN][1000 genomes]
rs3763728	0.89[ASN][1000 genomes]
rs3793786	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3793788	0.98[ASN][1000 genomes]
rs4012459	0.90[ASN][1000 genomes]
rs4240507	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4240508	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4253009	0.94[ASN][1000 genomes]
rs4253024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4253082	0.98[ASN][1000 genomes]
rs4253226	0.91[ASN][1000 genomes]
rs56002988	0.89[ASN][1000 genomes]
rs57761316	0.90[ASN][1000 genomes]
rs59219652	0.90[ASN][1000 genomes]
rs61288726	0.90[ASN][1000 genomes]
rs6537537	0.90[ASN][1000 genomes]
rs7080607	0.90[ASN][1000 genomes]
rs7082895	0.94[ASN][1000 genomes]
rs7087700	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7096755	0.89[ASN][1000 genomes]
rs7100059	0.80[ASN][1000 genomes]
rs7901433	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv831867	chr10:50607857-50788751	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50717200-50746000	Weak transcription	Fetal Heart	heart
2	chr10:50720400-50746200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:50723000-50741000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr10:50723200-50741000	Strong transcription	Primary T cells from cord blood	blood
5	chr10:50723200-50741000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr10:50723200-50741000	Strong transcription	HMEC	breast
7	chr10:50723200-50741800	Strong transcription	Osteobl	bone
8	chr10:50723400-50739600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr10:50723400-50741000	Strong transcription	Fetal Intestine Large	intestine
10	chr10:50723400-50741000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr10:50723400-50741600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr10:50723400-50741600	Strong transcription	NHEK	skin
13	chr10:50723600-50741000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr10:50725000-50746200	Weak transcription	Psoas Muscle	Psoas
15	chr10:50726800-50739600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:50727800-50741000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr10:50727800-50741000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr10:50727800-50741000	Strong transcription	Adipose Nuclei	Adipose
19	chr10:50727800-50741200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr10:50728200-50741000	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr10:50728200-50741400	Strong transcription	HSMM	muscle
22	chr10:50728400-50741000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr10:50728400-50741000	Strong transcription	Placenta	Placenta
24	chr10:50728600-50740600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr10:50728600-50741400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr10:50728800-50741000	Strong transcription	Dnd41	blood
27	chr10:50728800-50742000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr10:50729000-50745800	Weak transcription	Stomach Mucosa	stomach
29	chr10:50729200-50741400	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr10:50729200-50742400	Strong transcription	Hela-S3	cervix
31	chr10:50729600-50740000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr10:50730000-50746400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr10:50730600-50741000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr10:50730600-50741200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr10:50730800-50741000	Strong transcription	Ovary	ovary
36	chr10:50730800-50741400	Strong transcription	Primary B cells from peripheral blood	blood
37	chr10:50731000-50740400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr10:50731000-50741400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr10:50731200-50740800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr10:50731200-50741000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr10:50731400-50740600	Strong transcription	NH-A	brain
42	chr10:50731400-50741000	Strong transcription	Liver	Liver
43	chr10:50731600-50740800	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr10:50731600-50741000	Strong transcription	Primary hematopoietic stem cells	blood
45	chr10:50731600-50746200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr10:50731800-50739600	Weak transcription	Brain Substantia Nigra	brain
47	chr10:50731800-50745800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr10:50732000-50741000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr10:50732000-50741000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr10:50732000-50741000	Strong transcription	Fetal Brain Female	brain

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