Variant report

Variant	rs3809313
Chromosome Location	chr12:121329967-121329968
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121324943..121326545-chr12:121329640..121331374,2	K562	blood:
2	chr12:121328082..121330885-chr12:121339869..121342050,3	MCF-7	breast:
3	chr12:121321411..121324329-chr12:121329045..121331159,2	MCF-7	breast:
4	chr12:121304739..121306957-chr12:121328981..121330571,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157837	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10774572	0.88[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10849791	0.84[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs10849807	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11065282	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065283	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065284	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065292	0.88[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065293	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065300	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11065307	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11065311	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065324	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11065332	0.84[ASN][1000 genomes]
rs1151849	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1151859	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1151862	0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11608262	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11611087	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168944	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168946	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168948	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168953	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1177585	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1179939	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12371178	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12372231	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12580949	0.91[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12809299	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12822123	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12825746	0.83[ASN][1000 genomes]
rs12831094	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13746	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1542859	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1696357	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1696390	0.86[ASN][1000 genomes]
rs1718188	0.88[ASN][1000 genomes]
rs2047568	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2393716	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2393717	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2650017	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2701177	0.88[ASN][1000 genomes]
rs2701184	0.90[ASN][1000 genomes]
rs2893876	0.83[EUR][1000 genomes]
rs3213566	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3213570	0.84[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs3213572	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs34009825	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34076777	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35600816	0.81[ASN][1000 genomes]
rs35706672	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35905305	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3842985	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3861797	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3883901	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3897746	0.87[CEU][hapmap];0.95[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]
rs3901854	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4454799	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs471688	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4766979	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4766980	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4767937	0.84[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4767941	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs487943	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs508595	0.96[CHB][hapmap];1.00[JPT][hapmap]
rs520753	0.87[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs531782	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs533264	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs548452	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs572016	0.83[ASN][1000 genomes]
rs577961	0.83[ASN][1000 genomes]
rs58291418	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58918988	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs590625	0.83[ASN][1000 genomes]
rs602984	0.91[ASN][1000 genomes]
rs609700	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs610694	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61946382	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61946383	0.87[ASN][1000 genomes]
rs61946384	0.88[ASN][1000 genomes]
rs61946385	0.87[ASN][1000 genomes]
rs61946386	0.87[ASN][1000 genomes]
rs624216	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs625228	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs647881	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs661647	0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs665585	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs666976	0.91[ASN][1000 genomes]
rs7137504	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs73413868	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73415720	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73415734	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7967190	0.83[ASN][1000 genomes]
rs7969140	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7980311	0.90[ASN][1000 genomes]
rs869781	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs904628	0.82[ASN][1000 genomes]
rs909053	0.84[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9431	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs989986	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs989987	0.85[EUR][1000 genomes];0.84[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	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
4	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3809313	SPPL3	cis	Adipose Subcutaneous	GTEx
rs3809313	SPPL3	cis	Nerve Tibial	GTEx
rs3809313	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs3809313	ACADS	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121288200-121339600	Weak transcription	Hela-S3	cervix
2	chr12:121294200-121340400	Weak transcription	HSMM	muscle
3	chr12:121297400-121339800	Weak transcription	A549	lung
4	chr12:121304600-121339800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:121306600-121331400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:121310800-121331400	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:121312600-121339800	Weak transcription	Brain Germinal Matrix	brain
8	chr12:121312600-121339800	Weak transcription	NHDF-Ad	bronchial
9	chr12:121313000-121332600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:121313400-121330000	Weak transcription	Psoas Muscle	Psoas
11	chr12:121313400-121332400	Weak transcription	Lung	lung
12	chr12:121313400-121339800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:121313400-121339800	Weak transcription	Pancreas	Pancrea
14	chr12:121315400-121332200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:121315800-121331400	Weak transcription	Fetal Stomach	stomach
16	chr12:121317200-121333400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:121317400-121338000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:121317600-121331400	Weak transcription	HepG2	liver
19	chr12:121317600-121339600	Weak transcription	HMEC	breast
20	chr12:121317800-121339600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:121318200-121339600	Weak transcription	NHEK	skin
22	chr12:121318200-121340400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:121323200-121340000	Weak transcription	Fetal Lung	lung
24	chr12:121323600-121330000	Weak transcription	Brain Angular Gyrus	brain
25	chr12:121323600-121330000	Weak transcription	Right Ventricle	heart
26	chr12:121323600-121331400	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:121323600-121332200	Weak transcription	Stomach Mucosa	stomach
28	chr12:121323600-121340600	Weak transcription	Aorta	Aorta
29	chr12:121324000-121340400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:121324400-121330000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:121324400-121330000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:121324400-121331400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:121324400-121334000	Weak transcription	Small Intestine	intestine
34	chr12:121324400-121339600	Weak transcription	Brain Substantia Nigra	brain
35	chr12:121324400-121339800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr12:121324600-121330000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:121324600-121330000	Weak transcription	Dnd41	blood
38	chr12:121324600-121339400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr12:121325000-121330000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr12:121325000-121331800	Weak transcription	Placenta	Placenta
41	chr12:121325200-121330000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr12:121325400-121332400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:121325400-121335200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:121325400-121335800	Weak transcription	Thymus	Thymus
45	chr12:121325600-121330000	Weak transcription	GM12878-XiMat	blood
46	chr12:121325800-121331400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:121325800-121338000	Weak transcription	Fetal Brain Female	brain
48	chr12:121325800-121339800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:121326000-121339800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:121326400-121330000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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