Variant report

Variant	rs661647
Chromosome Location	chr12:121282659-121282660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1039302	0.80[YRI][hapmap]
rs10774572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10849786	0.80[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]
rs11065264	0.81[ASN][1000 genomes]
rs11065282	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065283	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065284	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065293	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
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]
rs11065324	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1151849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1151859	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1151862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11608262	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11611087	1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168944	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168946	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168948	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168953	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1177585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1179939	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12371178	0.83[ASN][1000 genomes]
rs12580949	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs12809299	0.81[AMR][1000 genomes];0.84[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	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.85[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];0.94[JPT][hapmap]
rs1718180	0.92[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];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2393717	0.96[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2461475	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650017	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2893876	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3213566	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3213567	0.81[ASN][1000 genomes]
rs3213570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3213572	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34009825	0.83[ASN][1000 genomes]
rs34076777	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35706672	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35905305	0.82[ASN][1000 genomes]
rs3809313	0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3842985	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3861797	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3883901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766979	0.82[AMR][1000 genomes];0.85[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	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs508595	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs520753	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs531782	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533264	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs548452	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs572016	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577961	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580240	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58291418	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58918988	0.82[ASN][1000 genomes]
rs590625	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602984	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs608394	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs609700	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs610694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs618482	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs624216	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]
rs625228	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs647881	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs665585	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs666976	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs668622	0.80[ASN][1000 genomes]
rs7137504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs73413868	0.84[ASN][1000 genomes]
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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs989986	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs989987	0.81[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs661647	SPPL3	cis	Adipose Subcutaneous	GTEx
rs661647	UNQ1887	cis	Temporal Cortex	GTEx
rs661647	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

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	chr12:121269800-121282800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:121269800-121291400	Weak transcription	Fetal Intestine Large	intestine
5	chr12:121272800-121285600	Weak transcription	Hela-S3	cervix
6	chr12:121273800-121282800	Weak transcription	Fetal Stomach	stomach
7	chr12:121274000-121284000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:121274000-121285800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:121274000-121287200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:121274200-121291800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr12:121274400-121282800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:121274400-121282800	Weak transcription	Brain Germinal Matrix	brain
13	chr12:121274400-121284800	Weak transcription	Primary B cells from cord blood	blood
14	chr12:121274400-121285200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:121274400-121285200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:121274400-121285400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:121274400-121285400	Weak transcription	Aorta	Aorta
18	chr12:121274400-121285800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:121274400-121289400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr12:121274600-121282800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:121274600-121282800	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:121274600-121285200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:121274600-121289000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:121274600-121289800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:121274800-121282800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:121274800-121282800	Weak transcription	Esophagus	oesophagus
27	chr12:121274800-121283000	Weak transcription	NHEK	skin
28	chr12:121274800-121284600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr12:121274800-121291800	Weak transcription	Dnd41	blood
30	chr12:121275000-121284600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:121275000-121284600	Weak transcription	Fetal Lung	lung
32	chr12:121276200-121282800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr12:121277600-121287200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr12:121278200-121283600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:121279200-121289200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:121279400-121283000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr12:121279400-121284000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:121279400-121286400	Enhancers	Brain Substantia Nigra	brain
39	chr12:121279600-121283000	Enhancers	Liver	Liver
40	chr12:121279600-121283200	Enhancers	Brain Angular Gyrus	brain
41	chr12:121279600-121286600	Enhancers	Brain Hippocampus Middle	brain
42	chr12:121279800-121282800	Enhancers	Brain Cingulate Gyrus	brain
43	chr12:121279800-121282800	Enhancers	GM12878-XiMat	blood
44	chr12:121279800-121284000	Enhancers	Brain Anterior Caudate	brain
45	chr12:121280200-121284600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:121280400-121283400	Enhancers	Pancreas	Pancrea
47	chr12:121280800-121284000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:121280800-121284000	Enhancers	Ovary	ovary
49	chr12:121280800-121284400	Weak transcription	HSMM	muscle
50	chr12:121280800-121287400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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