Variant report

Variant	rs1601852
Chromosome Location	chr3:112235472-112235473
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1105938	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1155073	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632867	0.81[CHB][hapmap]
rs1386895	0.81[CHB][hapmap]
rs1398091	0.92[JPT][hapmap]
rs1488259	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1814052	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1844089	0.83[CHB][hapmap]
rs1873571	0.81[CHB][hapmap]
rs1873572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2171513	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2171514	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2292442	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2633556	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2633557	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2633560	0.83[ASN][1000 genomes]
rs2633562	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2633563	0.83[ASN][1000 genomes]
rs2633574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2633575	0.95[ASN][1000 genomes]
rs2633578	0.81[CHB][hapmap]
rs2633579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2633580	0.81[CHB][hapmap]
rs2633582	0.83[CHB][hapmap]
rs2633588	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2633589	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2638013	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2638015	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2638016	0.83[CHB][hapmap]
rs2638017	0.83[CHB][hapmap]
rs2638019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2638022	0.81[CHB][hapmap]
rs2638023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2638026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2638028	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638031	0.81[CHB][hapmap]
rs2638032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2638035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638037	0.81[CHB][hapmap]
rs2638039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2668219	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705505	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2705507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2705515	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705517	0.81[CHB][hapmap]
rs2705518	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705519	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2705521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2705522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2705525	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2705533	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2705534	0.81[CHB][hapmap]
rs2705535	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2705536	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2705541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2705544	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2705548	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2705552	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2705555	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2705556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2705559	0.83[CHB][hapmap]
rs2705560	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2705564	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2705566	0.86[CHB][hapmap]
rs2933134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2933135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2933137	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2942061	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2952319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2952320	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2952323	0.83[CHB][hapmap]
rs2952324	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2952325	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2952326	0.83[CHB][hapmap]
rs2952327	0.83[CHB][hapmap]
rs2969895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2969896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2971204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3112268	0.99[ASN][1000 genomes]
rs728568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs751875	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs766969	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9869455	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs9869579	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs998036	0.93[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1601852	SCGB2A2	trans	brain	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112218800-112241600	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr3:112227400-112269800	Weak transcription	Small Intestine	intestine
3	chr3:112231600-112246800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:112233400-112236600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr3:112233800-112236600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:112233800-112236800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:112233800-112236800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr3:112233800-112237000	Weak transcription	Primary B cells from cord blood	blood
9	chr3:112233800-112237800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:112234000-112237600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:112234000-112247600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:112234200-112272000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:112235200-112235600	Enhancers	Primary hematopoietic stem cells	blood
14	chr3:112235200-112236200	ZNF genes & repeats	GM12878-XiMat	blood
15	chr3:112235400-112235600	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr3:112235400-112235800	Enhancers	Primary B cells from peripheral blood	blood
17	chr3:112235400-112235800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:112235400-112235800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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