Variant report

Variant	rs2393717
Chromosome Location	chr12:121220375-121220376
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121211334..121215369-chr12:121217344..121221098,3	K562	blood:
2	chr12:121219382..121222529-chr12:121225317..121227004,3	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10774572	0.96[CHB][hapmap];1.00[JPT][hapmap]
rs10849791	0.96[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10849807	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11065264	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11065282	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11065283	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11065284	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11065292	0.96[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11065293	0.82[ASN][1000 genomes]
rs11065300	0.96[CHB][hapmap];1.00[JPT][hapmap]
rs11065311	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11065324	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1151849	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1151862	0.96[CHB][hapmap];1.00[JPT][hapmap]
rs11608262	0.82[ASN][1000 genomes]
rs11611087	0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1177585	0.96[CHB][hapmap];1.00[JPT][hapmap]
rs12579868	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12580949	0.96[CHB][hapmap];0.90[JPT][hapmap]
rs12809299	0.81[ASN][1000 genomes]
rs12822123	0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12825746	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13746	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1467283	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1542859	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1696357	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2015462	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2047568	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2893876	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3213566	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213570	0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3213572	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34076777	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs35706672	0.82[ASN][1000 genomes]
rs3809313	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3842985	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3861797	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3883901	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3897746	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3901854	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4454799	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs471688	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4766979	0.82[ASN][1000 genomes]
rs4767937	0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs508595	0.96[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs520753	0.87[CHB][hapmap]
rs525425	0.96[ASN][1000 genomes]
rs531782	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs534415	0.96[ASN][1000 genomes]
rs572016	0.81[ASN][1000 genomes]
rs577961	0.81[ASN][1000 genomes]
rs580240	0.94[ASN][1000 genomes]
rs58291418	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs590625	0.81[ASN][1000 genomes]
rs608394	0.94[ASN][1000 genomes]
rs610694	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs618482	0.94[ASN][1000 genomes]
rs624216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs625228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs661647	0.96[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs668622	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7137504	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7305849	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs869781	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs909053	0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9431	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs989986	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs989987	0.82[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2393717	UNQ1887	cis	Frontal Cortex	GTEx
rs2393717	SPPL3	cis	Adipose Subcutaneous	GTEx
rs2393717	SPPL3	cis	Nerve Tibial	GTEx
rs2393717	UNQ1887	cis	Temporal Cortex	GTEx
rs2393717	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121197800-121220400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr12:121198400-121220800	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr12:121200600-121222600	Strong transcription	Fetal Muscle Trunk	muscle
4	chr12:121205200-121221000	Weak transcription	Stomach Mucosa	stomach
5	chr12:121206200-121238600	Weak transcription	Small Intestine	intestine
6	chr12:121206600-121220400	Weak transcription	NH-A	brain
7	chr12:121206600-121220600	Weak transcription	NHLF	lung
8	chr12:121206800-121220600	Weak transcription	Hela-S3	cervix
9	chr12:121207000-121223800	Weak transcription	Pancreas	Pancrea
10	chr12:121207200-121220400	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:121207200-121220400	Weak transcription	HMEC	breast
12	chr12:121207200-121220400	Weak transcription	NHEK	skin
13	chr12:121207200-121221800	Weak transcription	Colonic Mucosa	Colon
14	chr12:121207200-121225000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:121207200-121226200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:121207200-121233000	Weak transcription	HSMMtube	muscle
17	chr12:121207400-121220800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr12:121209200-121224200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:121209400-121236800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:121209600-121220400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:121209600-121220600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:121209800-121223400	Strong transcription	Fetal Thymus	thymus
23	chr12:121210400-121220600	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr12:121211400-121260800	Weak transcription	Gastric	stomach
25	chr12:121211800-121221800	Weak transcription	Lung	lung
26	chr12:121212600-121221800	Weak transcription	Spleen	Spleen
27	chr12:121212600-121229600	Weak transcription	Right Atrium	heart
28	chr12:121212600-121229800	Weak transcription	Right Ventricle	heart
29	chr12:121212600-121236600	Weak transcription	Fetal Heart	heart
30	chr12:121212800-121220400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:121212800-121228000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr12:121213200-121222200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:121213200-121231200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:121213400-121220600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr12:121213400-121224800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr12:121213600-121223000	Strong transcription	Dnd41	blood
37	chr12:121214000-121220400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr12:121214000-121221000	Strong transcription	Primary hematopoietic stem cells	blood
39	chr12:121214000-121221800	Weak transcription	Psoas Muscle	Psoas
40	chr12:121215000-121221200	Weak transcription	Brain Angular Gyrus	brain
41	chr12:121215000-121222800	Strong transcription	Liver	Liver
42	chr12:121215000-121224200	Weak transcription	Brain Substantia Nigra	brain
43	chr12:121215200-121222800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:121215400-121220400	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr12:121215600-121220600	Strong transcription	Fetal Intestine Small	intestine
46	chr12:121215600-121220600	Strong transcription	Fetal Stomach	stomach
47	chr12:121215600-121222800	Strong transcription	Thymus	Thymus
48	chr12:121216400-121221000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:121216400-121222800	Strong transcription	Fetal Intestine Large	intestine
50	chr12:121216600-121221000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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