Variant report

Variant	rs12254548
Chromosome Location	chr10:26987060-26987061
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:26985323..26988042-chr10:27148387..27150466,3	MCF-7	breast:
2	chr10:26986021..26987940-chr10:27149008..27151636,2	MCF-7	breast:
3	chr10:26985918..26987566-chr10:27148462..27151237,2	K562	blood:
4	chr10:26985752..26988058-chr10:26992017..26994907,3	MCF-7	breast:
5	chr10:26986198..26989615-chr10:27022506..27024765,3	MCF-7	breast:
6	chr10:26986066..26987689-chr10:27148181..27149962,2	K562	blood:
7	chr10:26986774..26988762-chr10:27020723..27023686,2	K562	blood:

Variant related genes	Relation type
ENSG00000136754	Chromatin interaction
ENSG00000148459	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10764636	0.80[EUR][1000 genomes]
rs11015223	0.94[ASN][1000 genomes]
rs11015232	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12415035	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1809359	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1960383	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35459290	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3808913	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68159164	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7069431	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7100327	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71483808	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7896301	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7904343	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][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	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv1798973	chr10:26968171-27001814	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv550233	chr10:26968171-27011323	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26985400-26988600	Active TSS	GM12878-XiMat	blood
2	chr10:26985600-26987200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:26985600-26987200	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr10:26985600-26987200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr10:26985600-26987200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr10:26985600-26987200	Active TSS	Colon Smooth Muscle	Colon
7	chr10:26985600-26987200	Active TSS	Fetal Brain Male	brain
8	chr10:26985600-26987200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr10:26985600-26987200	Active TSS	Right Atrium	heart
10	chr10:26985600-26987200	Active TSS	Right Ventricle	heart
11	chr10:26985600-26987200	Active TSS	NH-A	brain
12	chr10:26985600-26987200	Active TSS	NHLF	lung
13	chr10:26985600-26987400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr10:26985600-26987400	Active TSS	Fetal Kidney	kidney
15	chr10:26985600-26987600	Active TSS	H1 Cell Line	embryonic stem cell
16	chr10:26985600-26987600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr10:26985600-26987600	Active TSS	Fetal Muscle Trunk	muscle
18	chr10:26985600-26987800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr10:26985600-26987800	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr10:26985600-26988000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr10:26985600-26988200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr10:26985600-26988200	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr10:26985600-26988200	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr10:26985600-26988200	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr10:26985600-26988200	Active TSS	A549	lung
26	chr10:26985600-26988400	Active TSS	Psoas Muscle	Psoas
27	chr10:26985800-26987200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr10:26985800-26987200	Active TSS	Aorta	Aorta
29	chr10:26985800-26987200	Active TSS	Brain Angular Gyrus	brain
30	chr10:26985800-26987200	Active TSS	Gastric	stomach
31	chr10:26985800-26987200	Active TSS	Lung	lung
32	chr10:26985800-26987200	Active TSS	Pancreas	Pancrea
33	chr10:26985800-26987400	Active TSS	Fetal Intestine Small	intestine
34	chr10:26985800-26987400	Active TSS	Small Intestine	intestine
35	chr10:26985800-26987600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr10:26985800-26987600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr10:26985800-26987600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr10:26985800-26987600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr10:26985800-26987600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr10:26985800-26987600	Active TSS	Esophagus	oesophagus
41	chr10:26985800-26987600	Active TSS	Fetal Heart	heart
42	chr10:26985800-26987800	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr10:26985800-26988000	Active TSS	Thymus	Thymus
44	chr10:26986000-26987200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr10:26986000-26987200	Active TSS	Primary monocytes fromperipheralblood	blood
46	chr10:26986000-26987200	Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr10:26986000-26987200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr10:26986000-26987200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
49	chr10:26986000-26987200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr10:26986000-26987200	Active TSS	Primary T helper cells PMA-I stimulated	--

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