Variant report

Variant	rs1917657
Chromosome Location	chr12:47515141-47515142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10785664	1.00[YRI][hapmap]
rs10785665	1.00[YRI][hapmap]
rs10785668	1.00[YRI][hapmap]
rs10881045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10881047	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10881069	1.00[YRI][hapmap]
rs10881070	1.00[YRI][hapmap]
rs11183738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183740	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11183741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183750	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs11183751	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11183752	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11183759	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11183760	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11183761	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11183777	0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs11183783	1.00[YRI][hapmap]
rs12368600	0.81[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12370192	1.00[ASW][hapmap];0.80[CEU][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.93[AMR][1000 genomes]
rs12370851	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1554693	1.00[YRI][hapmap]
rs17222290	1.00[ASW][hapmap];0.81[CEU][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes]
rs17821774	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs1917655	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1917656	0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2408718	0.84[ASW][hapmap]
rs4768142	1.00[ASW][hapmap];0.81[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs4768143	1.00[YRI][hapmap]
rs4768779	1.00[YRI][hapmap]
rs4768781	1.00[YRI][hapmap]
rs4768782	1.00[YRI][hapmap]
rs73101453	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73108103	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73108123	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs732523	0.84[ASW][hapmap]
rs7955924	0.84[EUR][1000 genomes]
rs7965849	0.84[EUR][1000 genomes]
rs7974410	0.84[ASW][hapmap]
rs952967	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][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	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1917657	DNAJC22	cis	cerebellum	SCAN
rs1917657	DHH	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47497400-47535200	Weak transcription	Aorta	Aorta
2	chr12:47505600-47528800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:47505800-47538600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr12:47506000-47535000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr12:47506200-47538400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:47506400-47516800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:47506800-47528800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr12:47507400-47532800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:47508400-47545200	Weak transcription	HSMMtube	muscle
10	chr12:47509200-47528800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:47509200-47529200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:47509400-47531800	Weak transcription	Primary T cells from cord blood	blood
13	chr12:47510200-47516400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:47514200-47515400	Enhancers	NHEK	skin
15	chr12:47514200-47515600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:47514400-47515200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:47514400-47515600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:47514400-47516200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:47514600-47515400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:47514600-47515400	Enhancers	NH-A	brain
21	chr12:47514600-47515600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr12:47514600-47516200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:47514600-47516200	Enhancers	HMEC	breast
24	chr12:47514800-47515200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:47514800-47515200	Enhancers	HSMM	muscle
26	chr12:47514800-47515200	Enhancers	NHLF	lung
27	chr12:47514800-47515400	Flanking Active TSS	A549	lung
28	chr12:47514800-47515600	Enhancers	Osteobl	bone
29	chr12:47514800-47516200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr12:47514800-47517000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:47514800-47518800	Enhancers	NHDF-Ad	bronchial
32	chr12:47515000-47516200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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