Variant report

Variant	rs624216
Chromosome Location	chr12:121278541-121278542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121271672..121273889-chr12:121276026..121278960,3	K562	blood:
2	chr12:121276148..121280406-chr12:121280762..121286205,4	K562	blood:
3	chr12:121276148..121279076-chr12:121280762..121283669,2	K562	blood:

Variant related genes	Relation type
ENSG00000157837	Chromatin interaction
ENSG00000213137	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1027556	0.84[YRI][hapmap]
rs1039302	0.86[YRI][hapmap]
rs10431387	0.86[YRI][hapmap]
rs10437838	0.86[YRI][hapmap]
rs10774568	0.81[YRI][hapmap]
rs10774569	0.85[YRI][hapmap]
rs10774571	0.85[YRI][hapmap]
rs10774572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10849788	0.81[YRI][hapmap]
rs10849791	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10849807	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10849810	0.84[YRI][hapmap]
rs10849811	0.85[YRI][hapmap]
rs11065259	0.85[YRI][hapmap]
rs11065264	0.81[ASN][1000 genomes]
rs11065282	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065283	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065284	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065293	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065298	0.85[YRI][hapmap]
rs11065300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11065307	0.83[ASN][1000 genomes]
rs11065311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11065322	0.86[YRI][hapmap]
rs11065324	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1151849	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1151859	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1151862	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11608262	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11611087	1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168944	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168946	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168948	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168953	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1177585	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1179939	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12371178	0.83[ASN][1000 genomes]
rs12580949	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs12809299	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12822123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12825746	0.98[ASN][1000 genomes]
rs12831094	0.84[ASN][1000 genomes]
rs13746	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1542859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1696357	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1718180	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2015462	0.81[ASN][1000 genomes]
rs2047568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2393717	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2393718	0.82[YRI][hapmap]
rs2461475	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650017	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2893876	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3213566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3213567	0.81[ASN][1000 genomes]
rs3213568	0.86[YRI][hapmap]
rs3213570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3213571	0.85[YRI][hapmap]
rs3213572	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34009825	0.83[ASN][1000 genomes]
rs34076777	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35706672	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35905305	0.82[ASN][1000 genomes]
rs3809313	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3809314	0.86[YRI][hapmap]
rs3842985	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3861797	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3883901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3897746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3901854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4454799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs471688	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766979	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4766980	0.84[ASN][1000 genomes]
rs4767937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs487943	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs508595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs520753	0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs531782	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533264	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs548452	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs572016	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577961	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580240	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58291418	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58918988	0.82[ASN][1000 genomes]
rs590625	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602984	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs608394	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs609700	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs610694	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs618482	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs625228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs647881	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6489780	0.86[YRI][hapmap]
rs6489782	0.82[YRI][hapmap]
rs661647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665585	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs666976	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs668622	0.80[ASN][1000 genomes]
rs7135147	0.86[YRI][hapmap]
rs7137504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7139145	0.85[YRI][hapmap]
rs715319	0.86[YRI][hapmap]
rs7298639	0.85[YRI][hapmap]
rs73413868	0.84[ASN][1000 genomes]
rs7965332	0.84[YRI][hapmap]
rs7969140	0.84[ASN][1000 genomes]
rs869781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs909053	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs989986	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs989987	0.83[AMR][1000 genomes];0.87[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
rs624216	RPLP0	cis	Skin Sun Exposed Lower leg	GTEx
rs624216	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121267200-121282800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:121267600-121285800	Weak transcription	Colonic Mucosa	Colon
3	chr12:121269800-121281200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:121269800-121281200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:121269800-121282800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:121269800-121291400	Weak transcription	Fetal Intestine Large	intestine
7	chr12:121272800-121285600	Weak transcription	Hela-S3	cervix
8	chr12:121273400-121281200	Weak transcription	K562	blood
9	chr12:121273800-121280200	Weak transcription	HSMMtube	muscle
10	chr12:121273800-121282800	Weak transcription	Fetal Stomach	stomach
11	chr12:121274000-121278800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:121274000-121279400	Weak transcription	Brain Anterior Caudate	brain
13	chr12:121274000-121284000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:121274000-121285800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:121274000-121287200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:121274200-121279400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:121274200-121279600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:121274200-121279600	Weak transcription	Brain Angular Gyrus	brain
19	chr12:121274200-121280400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:121274200-121282200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:121274200-121291800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr12:121274400-121280400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:121274400-121280400	Weak transcription	Right Atrium	heart
24	chr12:121274400-121280600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:121274400-121282000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:121274400-121282200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr12:121274400-121282600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr12:121274400-121282800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr12:121274400-121282800	Weak transcription	Brain Germinal Matrix	brain
30	chr12:121274400-121284800	Weak transcription	Primary B cells from cord blood	blood
31	chr12:121274400-121285200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr12:121274400-121285200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:121274400-121285400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:121274400-121285400	Weak transcription	Aorta	Aorta
35	chr12:121274400-121285800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:121274400-121289400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr12:121274600-121279400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:121274600-121279400	Weak transcription	Adipose Nuclei	Adipose
39	chr12:121274600-121279400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:121274600-121279400	Weak transcription	Brain Substantia Nigra	brain
41	chr12:121274600-121279600	Weak transcription	Liver	Liver
42	chr12:121274600-121281200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr12:121274600-121281200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:121274600-121281600	Weak transcription	Lung	lung
45	chr12:121274600-121282000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr12:121274600-121282200	Weak transcription	Spleen	Spleen
47	chr12:121274600-121282800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr12:121274600-121282800	Weak transcription	Fetal Muscle Leg	muscle
49	chr12:121274600-121285200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:121274600-121289000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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