Variant report

Variant	rs580240
Chromosome Location	chr12:121199903-121199904
allele	G/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	POLR2A	chr12:121199874-121199992	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:121199470..121201795-chr12:121202855..121205373,2	MCF-7	breast:
2	chr1:45186381..45189343-chr12:121198720..121200674,2	K562	blood:
3	chr12:121167755..121169709-chr12:121199569..121201088,2	K562	blood:

Variant related genes	Relation type
ENSG00000255946	TF binding region
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10849791	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11065264	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12579868	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13746	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1467283	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1718180	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2015462	0.95[ASN][1000 genomes]
rs2047568	0.85[ASN][1000 genomes]
rs2393717	0.94[ASN][1000 genomes]
rs2461475	0.80[EUR][1000 genomes]
rs2893876	0.85[ASN][1000 genomes]
rs3213566	0.94[ASN][1000 genomes]
rs3213567	0.94[ASN][1000 genomes]
rs3213570	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3213572	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3842985	0.83[ASN][1000 genomes]
rs3861797	0.83[ASN][1000 genomes]
rs3883901	0.83[ASN][1000 genomes]
rs3901854	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs471688	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4767937	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs487943	0.81[EUR][1000 genomes]
rs494632	0.86[EUR][1000 genomes]
rs508595	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520753	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs525425	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs531782	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs533264	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs534415	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs548452	0.81[EUR][1000 genomes]
rs572016	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs577961	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs590625	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs602984	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs608394	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609700	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs610694	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs618482	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624216	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs625228	0.80[ASN][1000 genomes]
rs647881	0.81[EUR][1000 genomes]
rs661647	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs665585	0.81[EUR][1000 genomes]
rs668622	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7137504	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7305849	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs909053	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9431	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1041153	chr12:121171986-121208826	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs580240	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs580240	RPLP0	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121194000-121200800	Weak transcription	HepG2	liver
2	chr12:121194200-121202200	Weak transcription	K562	blood
3	chr12:121195000-121201200	Weak transcription	Small Intestine	intestine
4	chr12:121195200-121200000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr12:121195600-121204200	Weak transcription	Stomach Mucosa	stomach
6	chr12:121195600-121207200	Strong transcription	Brain Germinal Matrix	brain
7	chr12:121196000-121201000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr12:121196200-121201000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:121196200-121201000	Weak transcription	Osteobl	bone
10	chr12:121196400-121207000	Strong transcription	Fetal Brain Female	brain
11	chr12:121196800-121200200	Enhancers	Psoas Muscle	Psoas
12	chr12:121196800-121201400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:121196800-121203000	Strong transcription	Fetal Intestine Large	intestine
14	chr12:121196800-121212800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:121197000-121200200	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:121197000-121203000	Strong transcription	Fetal Intestine Small	intestine
17	chr12:121197000-121207200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:121197200-121200800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:121197200-121201200	Weak transcription	Ovary	ovary
20	chr12:121197200-121204200	Weak transcription	Fetal Brain Male	brain
21	chr12:121197200-121210000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:121197400-121200200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr12:121197400-121201000	Genic enhancers	Fetal Thymus	thymus
24	chr12:121197400-121201200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:121197400-121203000	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr12:121197400-121203400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:121197400-121203400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:121197400-121203800	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:121197400-121207000	Strong transcription	Pancreas	Pancrea
30	chr12:121197400-121209800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:121197400-121212600	Strong transcription	Thymus	Thymus
32	chr12:121197400-121220000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr12:121197600-121203000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr12:121197600-121204400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:121197600-121205400	Strong transcription	GM12878-XiMat	blood
36	chr12:121197600-121207200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:121197600-121210400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:121197800-121200000	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr12:121197800-121200000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr12:121197800-121201000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr12:121197800-121203400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr12:121197800-121209000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:121197800-121212400	Strong transcription	Liver	Liver
44	chr12:121197800-121220400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr12:121198000-121200000	Genic enhancers	Brain Inferior Temporal Lobe	brain
46	chr12:121198000-121201200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:121198000-121201400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:121198000-121202600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:121198000-121207200	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr12:121198000-121207200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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