Variant report

Variant	rs3901854
Chromosome Location	chr12:121225526-121225527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121224775..121227076-chr12:121227465..121229261,2	K562	blood:
2	chr12:121219382..121222529-chr12:121225317..121227004,3	K562	blood:
3	chr12:121223533..121225993-chr12:121234568..121236764,2	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10774572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10849791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11065264	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065283	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065284	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065293	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs11065311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11065324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs1151849	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs1151862	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11608262	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11611087	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1177585	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12579868	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12580949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs12809299	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12822123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12824150	0.85[CEU][hapmap]
rs12825746	0.83[ASN][1000 genomes]
rs13746	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1467283	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1542859	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap]
rs1696357	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs2015462	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2047568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2062507	0.85[CEU][hapmap];0.81[MKK][hapmap]
rs2393717	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2893876	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3213566	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3213567	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3213570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3213572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34076777	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35706672	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3809313	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3842985	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3861797	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3883901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3897746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs4454799	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs471688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4766979	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4766980	0.80[AMR][1000 genomes]
rs4767935	0.85[CEU][hapmap];0.81[MKK][hapmap]
rs4767937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs494632	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs508595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs520753	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs525425	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs531782	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs534415	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs572016	0.82[ASN][1000 genomes]
rs577961	0.82[ASN][1000 genomes]
rs580240	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58291418	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs590625	0.82[ASN][1000 genomes]
rs608394	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs610694	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs618482	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs624216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs625228	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs661647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs668622	0.95[ASN][1000 genomes]
rs7137504	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7305849	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs869781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs909053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9431	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs989986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs989987	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3901854	SPPL3	cis	parietal	SCAN
rs3901854	HPD	cis	parietal	SCAN
rs3901854	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs3901854	ACADS	cis	Thyroid	GTEx
rs3901854	WSB2	cis	cerebellum	SCAN
rs3901854	MLEC	cis	lymphoblastoid	seeQTL
rs3901854	P2RX4	cis	cerebellum	SCAN
rs3901854	SRRM4	cis	cerebellum	SCAN
rs3901854	SPPL3	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121206200-121238600	Weak transcription	Small Intestine	intestine
2	chr12:121207200-121226200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:121207200-121233000	Weak transcription	HSMMtube	muscle
4	chr12:121209400-121236800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:121211400-121260800	Weak transcription	Gastric	stomach
6	chr12:121212600-121229600	Weak transcription	Right Atrium	heart
7	chr12:121212600-121229800	Weak transcription	Right Ventricle	heart
8	chr12:121212600-121236600	Weak transcription	Fetal Heart	heart
9	chr12:121212800-121228000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:121213200-121231200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:121221000-121225600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:121221000-121227800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:121221000-121250000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:121221200-121226200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:121221200-121226400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:121221200-121229600	Weak transcription	Osteobl	bone
17	chr12:121221200-121233000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:121221200-121233600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:121221200-121249400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:121221400-121225600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:121221400-121228200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:121221400-121229800	Weak transcription	NHDF-Ad	bronchial
23	chr12:121221400-121230400	Weak transcription	HMEC	breast
24	chr12:121221400-121231000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:121221400-121232800	Weak transcription	A549	lung
26	chr12:121221400-121235800	Weak transcription	Hela-S3	cervix
27	chr12:121221400-121240800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr12:121221600-121238800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr12:121222000-121227800	Weak transcription	Fetal Intestine Small	intestine
30	chr12:121222000-121229400	Weak transcription	Brain Anterior Caudate	brain
31	chr12:121222000-121233200	Weak transcription	NHEK	skin
32	chr12:121222000-121233800	Weak transcription	Fetal Stomach	stomach
33	chr12:121222200-121225600	Weak transcription	Left Ventricle	heart
34	chr12:121222200-121225800	Weak transcription	Fetal Lung	lung
35	chr12:121222200-121227800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:121222200-121228000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:121222200-121229400	Weak transcription	HepG2	liver
38	chr12:121222200-121230200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:121222200-121231200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:121222200-121231200	Weak transcription	Fetal Brain Female	brain
41	chr12:121222200-121237200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:121222200-121274000	Weak transcription	Lung	lung
43	chr12:121222400-121227400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr12:121222400-121229600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:121222400-121231200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:121222400-121238800	Weak transcription	Placenta	Placenta
47	chr12:121222400-121240400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:121222600-121225600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr12:121222600-121225600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr12:121222600-121226200	Weak transcription	Fetal Kidney	kidney

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