Variant report

Variant	rs12131820
Chromosome Location	chr1:58980232-58980233
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:58980196..58982472-chr1:59010665..59013532,3	K562	blood:
2	chr1:58980068..58984946-chr1:59009603..59013754,8	K562	blood:
3	chr1:58977602..58982967-chr1:59116778..59119321,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162600	Chromatin interaction
ENSG00000173406	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11207241	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12139614	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2271004	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6587822	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs697594	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs697595	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[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	nsv1008968	chr1:58582159-58982440	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv534974	chr1:58582159-58982440	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh 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
4	nsv998092	chr1:58978327-59002319	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58931200-59010800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:58933800-58984800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:58934800-58994000	Weak transcription	HSMM	muscle
4	chr1:58946400-58993800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:58953200-58986000	Weak transcription	Colonic Mucosa	Colon
6	chr1:58953600-58999200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:58955000-58986400	Weak transcription	Gastric	stomach
8	chr1:58955000-58988200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:58963800-58999000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:58964800-58986400	Weak transcription	K562	blood
11	chr1:58966600-59010600	Weak transcription	Placenta	Placenta
12	chr1:58967600-59010600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:58968200-58986400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:58968400-58984600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:58973800-58980600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr1:58974600-58987600	Weak transcription	Right Ventricle	heart
17	chr1:58974800-58981800	Weak transcription	Brain Substantia Nigra	brain
18	chr1:58974800-58984600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:58974800-58984600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:58974800-58984800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:58974800-58991600	Weak transcription	Esophagus	oesophagus
22	chr1:58974800-59005000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:58974800-59010800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:58974800-59011800	Weak transcription	Spleen	Spleen
25	chr1:58975000-59010600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:58975000-59010800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:58976600-58980600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:58976800-58980400	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:58977000-58980800	Strong transcription	Primary T cells from cord blood	blood
30	chr1:58977000-58980800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:58977000-58993000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr1:58977200-58980800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:58977200-58981800	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:58977200-58982400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:58977200-58984600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:58977200-58994000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:58977200-59005000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:58977200-59010800	Weak transcription	Brain Angular Gyrus	brain
39	chr1:58977200-59011400	Weak transcription	Ovary	ovary
40	chr1:58977400-58980400	Weak transcription	Pancreas	Pancrea
41	chr1:58977400-58980800	Strong transcription	Primary B cells from cord blood	blood
42	chr1:58977400-58981800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:58977400-58982200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:58977400-58982200	Weak transcription	HSMMtube	muscle
45	chr1:58977400-58982400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:58977400-58983400	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr1:58977400-58984800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr1:58977400-58987400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:58977400-58988600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:58977400-58989400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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