Variant report

Variant	rs12254451
Chromosome Location	chr10:90654795-90654796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10509555	1.00[EUR][1000 genomes]
rs10509556	1.00[EUR][1000 genomes]
rs10509558	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10509559	1.00[EUR][1000 genomes]
rs10509560	1.00[TSI][hapmap]
rs11202880	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11202881	1.00[ASW][hapmap];0.83[CHD][hapmap];0.84[LWK][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11202885	1.00[EUR][1000 genomes]
rs12242274	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12243282	1.00[EUR][1000 genomes]
rs12243621	1.00[EUR][1000 genomes]
rs12245525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12245668	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]
rs12257540	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12260572	1.00[EUR][1000 genomes]
rs12262249	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12263461	1.00[ASW][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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264141	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12269097	0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12413277	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12414800	1.00[EUR][1000 genomes]
rs17113311	1.00[EUR][1000 genomes]
rs17113344	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17113363	1.00[EUR][1000 genomes]
rs17113426	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17113457	1.00[EUR][1000 genomes]
rs17113476	1.00[EUR][1000 genomes]
rs17113724	1.00[EUR][1000 genomes]
rs17113812	0.86[ASN][1000 genomes]
rs17113942	1.00[EUR][1000 genomes]
rs17113959	1.00[EUR][1000 genomes]
rs17114000	1.00[EUR][1000 genomes]
rs17114016	1.00[EUR][1000 genomes]
rs17114020	1.00[EUR][1000 genomes]
rs17114024	1.00[EUR][1000 genomes]
rs17114057	1.00[EUR][1000 genomes]
rs17114116	1.00[TSI][hapmap]
rs17114283	1.00[TSI][hapmap]
rs1926184	0.81[AFR][1000 genomes]
rs1926185	0.81[AFR][1000 genomes]
rs2231780	1.00[EUR][1000 genomes]
rs2231785	1.00[EUR][1000 genomes]
rs2231786	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2282122	1.00[EUR][1000 genomes]
rs35996190	1.00[EUR][1000 genomes]
rs3781206	1.00[TSI][hapmap]
rs3814691	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3816245	1.00[TSI][hapmap]
rs3898173	1.00[EUR][1000 genomes]
rs3898174	1.00[EUR][1000 genomes]
rs4145761	0.94[ASN][1000 genomes]
rs56998609	1.00[EUR][1000 genomes]
rs57063754	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs58673564	1.00[EUR][1000 genomes]
rs58986570	1.00[EUR][1000 genomes]
rs59661152	1.00[EUR][1000 genomes]
rs60349051	1.00[EUR][1000 genomes]
rs60523093	1.00[EUR][1000 genomes]
rs7076879	1.00[ASW][hapmap];0.84[CHD][hapmap];0.81[LWK][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7077019	1.00[ASW][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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090604	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]
rs7098246	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73364839	1.00[EUR][1000 genomes]
rs73364841	1.00[EUR][1000 genomes]
rs73364851	1.00[EUR][1000 genomes]
rs74150104	0.86[ASN][1000 genomes]
rs7899463	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs7908852	1.00[TSI][hapmap]
rs7910708	1.00[ASW][hapmap];0.84[CHD][hapmap];0.81[LWK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7911566	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs7913997	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]
rs952323	0.92[AFR][1000 genomes];0.90[AMR][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	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12254451	CYP1B1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90641400-90658600	Weak transcription	Brain Angular Gyrus	brain
2	chr10:90641800-90656400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr10:90641800-90661800	Weak transcription	Thymus	Thymus
4	chr10:90642000-90684800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr10:90642000-90686400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr10:90642200-90656600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr10:90642800-90656400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr10:90646800-90656200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr10:90646800-90656800	Weak transcription	Psoas Muscle	Psoas
10	chr10:90647400-90656000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr10:90647400-90675200	Weak transcription	Spleen	Spleen
12	chr10:90647400-90681000	Weak transcription	Aorta	Aorta
13	chr10:90648000-90656000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr10:90648200-90654800	Weak transcription	Left Ventricle	heart
15	chr10:90648400-90656200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:90650000-90656200	Weak transcription	Fetal Stomach	stomach
17	chr10:90650800-90656400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr10:90651000-90655000	Enhancers	A549	lung
19	chr10:90651600-90656000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr10:90651800-90655200	Enhancers	Small Intestine	intestine
21	chr10:90652000-90658200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr10:90652200-90656000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr10:90652400-90654800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr10:90652400-90655800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr10:90652400-90656200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr10:90652400-90656200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr10:90652400-90656200	Weak transcription	Ovary	ovary
28	chr10:90652400-90656400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr10:90652400-90656600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr10:90652400-90656600	Weak transcription	HSMMtube	muscle
31	chr10:90652400-90656800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr10:90652400-90663000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr10:90652600-90656400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr10:90652600-90656600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr10:90652600-90656600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr10:90652600-90656800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr10:90652600-90656800	Weak transcription	NH-A	brain
38	chr10:90652600-90657000	Weak transcription	Brain Substantia Nigra	brain
39	chr10:90652600-90660800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr10:90652600-90661400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr10:90652800-90661200	Weak transcription	NHEK	skin
42	chr10:90652800-90661800	Weak transcription	HMEC	breast
43	chr10:90653200-90655200	Enhancers	Fetal Muscle Leg	muscle
44	chr10:90653400-90655400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr10:90653400-90655800	Strong transcription	Primary B cells from peripheral blood	blood
46	chr10:90653400-90656400	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr10:90653400-90656400	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr10:90653600-90655200	Strong transcription	Primary T cells from cord blood	blood
49	chr10:90653600-90655200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr10:90653600-90655800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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