Variant report

Variant	rs590625
Chromosome Location	chr12:121288923-121288924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121280705..121284627-chr12:121285918..121289462,3	K562	blood:
2	chr12:121261119..121262624-chr12:121287692..121289232,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213137	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10774572	0.84[ASN][1000 genomes]
rs10849791	0.82[ASN][1000 genomes]
rs10849807	0.84[ASN][1000 genomes]
rs11065264	0.81[ASN][1000 genomes]
rs11065282	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065283	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065284	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065292	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065293	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065300	0.84[ASN][1000 genomes]
rs11065307	0.83[ASN][1000 genomes]
rs11065311	0.83[ASN][1000 genomes]
rs1151849	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1151859	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1151862	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11608262	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11611087	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168944	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168946	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168948	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168953	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1177585	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1179939	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12371178	0.83[ASN][1000 genomes]
rs12580949	0.84[ASN][1000 genomes]
rs12809299	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12822123	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12825746	0.98[ASN][1000 genomes]
rs12831094	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13746	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1542859	0.83[ASN][1000 genomes]
rs1718180	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2015462	0.81[ASN][1000 genomes]
rs2047568	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2393717	0.81[ASN][1000 genomes]
rs2461475	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650017	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2893876	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3213566	0.81[ASN][1000 genomes]
rs3213567	0.81[ASN][1000 genomes]
rs3213570	0.81[ASN][1000 genomes]
rs34009825	0.83[ASN][1000 genomes]
rs34076777	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35706672	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35905305	0.82[ASN][1000 genomes]
rs3809313	0.83[ASN][1000 genomes]
rs3842985	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3861797	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3883901	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3897746	0.83[ASN][1000 genomes]
rs3901854	0.82[ASN][1000 genomes]
rs4454799	0.84[ASN][1000 genomes]
rs471688	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766979	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4766980	0.84[ASN][1000 genomes]
rs4767937	0.81[ASN][1000 genomes]
rs487943	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs508595	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs520753	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs531782	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533264	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs548452	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs572016	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577961	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580240	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58291418	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58918988	0.82[ASN][1000 genomes]
rs602984	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs608394	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs609700	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs610694	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs618482	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs624216	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625228	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs647881	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs661647	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665585	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs666976	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs668622	0.80[ASN][1000 genomes]
rs7137504	0.81[ASN][1000 genomes]
rs73413868	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7969140	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs869781	0.81[ASN][1000 genomes]
rs909053	0.82[ASN][1000 genomes]
rs9431	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs989986	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs989987	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
rs590625	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs590625	RPLP0	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121269800-121291400	Weak transcription	Fetal Intestine Large	intestine
2	chr12:121274200-121291800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:121274400-121289400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr12:121274600-121289000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:121274600-121289800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:121274800-121291800	Weak transcription	Dnd41	blood
7	chr12:121279200-121289200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:121281600-121296200	Weak transcription	HepG2	liver
9	chr12:121282000-121308600	Weak transcription	Fetal Kidney	kidney
10	chr12:121283200-121289200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr12:121283200-121291200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:121283200-121310200	Weak transcription	Placenta	Placenta
13	chr12:121283400-121289400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:121283400-121289400	Weak transcription	Fetal Muscle Leg	muscle
15	chr12:121283400-121291800	Weak transcription	Pancreas	Pancrea
16	chr12:121283400-121307400	Weak transcription	Esophagus	oesophagus
17	chr12:121283600-121290800	Weak transcription	Gastric	stomach
18	chr12:121283600-121295600	Weak transcription	Fetal Stomach	stomach
19	chr12:121283600-121302200	Weak transcription	Lung	lung
20	chr12:121284000-121289200	Weak transcription	Thymus	Thymus
21	chr12:121284000-121294400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:121284600-121292800	Enhancers	Primary B cells from peripheral blood	blood
23	chr12:121285000-121289200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:121285000-121290800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:121285200-121289600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:121285600-121289400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:121285600-121289400	Enhancers	A549	lung
28	chr12:121285600-121290000	Enhancers	Fetal Heart	heart
29	chr12:121285800-121289200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:121286000-121289000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:121286000-121289000	Weak transcription	Spleen	Spleen
32	chr12:121286000-121291800	Weak transcription	Fetal Intestine Small	intestine
33	chr12:121286200-121289200	Weak transcription	Brain Anterior Caudate	brain
34	chr12:121286200-121289400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr12:121286200-121289400	Weak transcription	Ovary	ovary
36	chr12:121286200-121289400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr12:121286200-121291400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:121286400-121289000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr12:121286400-121289000	Enhancers	GM12878-XiMat	blood
40	chr12:121286400-121290800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:121286400-121291000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr12:121286400-121291000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:121286400-121291200	Weak transcription	K562	blood
44	chr12:121286400-121293800	Weak transcription	Right Ventricle	heart
45	chr12:121286600-121289200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:121286600-121293600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:121286800-121289000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:121286800-121291200	Weak transcription	Primary T cells from cord blood	blood
49	chr12:121287000-121290000	Enhancers	Brain Hippocampus Middle	brain
50	chr12:121287400-121290000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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