Variant report

Variant	rs12938397
Chromosome Location	chr17:16186100-16186101
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1029809	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs10852834	0.91[EUR][1000 genomes]
rs11078337	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11650283	0.85[TSI][hapmap]
rs11650427	0.81[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs11650956	0.92[EUR][1000 genomes]
rs11651578	0.96[EUR][1000 genomes]
rs11653650	0.88[EUR][1000 genomes]
rs11654658	0.82[CEU][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs11655325	0.82[EUR][1000 genomes]
rs11656811	0.81[CEU][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs11868284	0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs12150564	0.90[EUR][1000 genomes]
rs12936233	0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs12936529	0.91[EUR][1000 genomes]
rs12938394	0.80[EUR][1000 genomes]
rs12938878	0.91[EUR][1000 genomes]
rs12939078	0.92[EUR][1000 genomes]
rs12945855	0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs12948244	0.82[EUR][1000 genomes]
rs12948905	0.82[EUR][1000 genomes]
rs1476810	0.85[TSI][hapmap]
rs15739	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs178657	0.90[MEX][hapmap]
rs178797	0.90[MEX][hapmap]
rs178820	0.90[MEX][hapmap]
rs178837	0.90[MEX][hapmap]
rs1963811	0.95[EUR][1000 genomes]
rs1989856	0.90[MEX][hapmap]
rs2014604	0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2109262	0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs2324306	0.91[EUR][1000 genomes]
rs2324307	0.94[EUR][1000 genomes]
rs3785620	0.86[EUR][1000 genomes]
rs3785621	0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs3785622	0.92[EUR][1000 genomes]
rs3785623	0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs3785625	0.95[EUR][1000 genomes]
rs3785626	0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs4791665	0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs4792728	0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs4792729	0.97[EUR][1000 genomes]
rs4792730	0.84[EUR][1000 genomes]
rs4792731	0.82[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs56326304	0.83[EUR][1000 genomes]
rs62072528	0.88[EUR][1000 genomes]
rs6502498	0.89[EUR][1000 genomes]
rs7210990	0.91[EUR][1000 genomes]
rs7215071	0.88[EUR][1000 genomes]
rs7219687	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs7225920	0.83[EUR][1000 genomes]
rs7477	0.80[GIH][hapmap];1.00[ASN][1000 genomes]
rs8074727	0.95[EUR][1000 genomes]
rs9747114	0.82[EUR][1000 genomes]
rs9890867	1.00[ASN][1000 genomes]
rs9902141	0.90[MEX][hapmap]
rs9903464	0.90[MEX][hapmap]
rs9909022	0.88[EUR][1000 genomes]
rs9910148	0.91[EUR][1000 genomes]
rs9914734	0.82[CEU][hapmap];0.96[EUR][1000 genomes]
rs9916220	0.88[EUR][1000 genomes]
rs9944524	0.82[CEU][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv907715	chr17:16019978-16206540	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
6	nsv907717	chr17:16076898-16239832	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
7	nsv528263	chr17:16097430-16196996	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
8	esv3326983	chr17:16138963-16210147	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs12938397	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs12938397	LOC125150	cis	normal skin	skin_eQTL
rs12938397	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs12938397	ELAC2	cis	parietal	SCAN
rs12938397	ZSWIM7	cis	Muscle Skeletal	GTEx
rs12938397	LOC125150	cis	uninvolved skin	skin_eQTL
rs12938397	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs12938397	CENPV	cis	Artery Tibial	GTEx
rs12938397	PIGL	cis	multi-tissue	Pritchard
rs12938397	ADORA2B	cis	Muscle Skeletal	GTEx
rs12938397	PRPSAP2	cis	parietal	SCAN
rs12938397	PRR6	cis	multi-tissue	Pritchard
rs12938397	TRPV2	cis	parietal	SCAN
rs12938397	ADORA2B	cis	Thyroid	GTEx
rs12938397	CENPV	cis	parietal	SCAN
rs12938397	ADORA2B	cis	Artery Tibial	GTEx
rs12938397	TTC19	cis	lymphoblastoid	seeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16159400-16189200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr17:16159600-16188800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr17:16159600-16189000	Weak transcription	Brain Anterior Caudate	brain
4	chr17:16160400-16188400	Weak transcription	Liver	Liver
5	chr17:16163400-16189200	Weak transcription	Left Ventricle	heart
6	chr17:16163600-16189200	Weak transcription	Pancreas	Pancrea
7	chr17:16164000-16189000	Weak transcription	Fetal Brain Female	brain
8	chr17:16164000-16189000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr17:16166200-16205400	Weak transcription	Brain Hippocampus Middle	brain
10	chr17:16168600-16188800	Weak transcription	Fetal Intestine Large	intestine
11	chr17:16171400-16188200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr17:16171400-16189000	Weak transcription	Spleen	Spleen
13	chr17:16171600-16188200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr17:16172600-16188200	Weak transcription	GM12878-XiMat	blood
15	chr17:16173000-16187800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr17:16173000-16188200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:16173200-16186800	Weak transcription	Fetal Lung	lung
18	chr17:16173200-16187800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr17:16173200-16188000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr17:16173400-16187800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr17:16173400-16187800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr17:16173400-16188200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr17:16175000-16189000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:16176200-16188800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr17:16179000-16189000	Weak transcription	Aorta	Aorta
26	chr17:16179800-16188800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr17:16180000-16188800	Weak transcription	Placenta	Placenta
28	chr17:16180800-16188200	Weak transcription	Adipose Nuclei	Adipose
29	chr17:16181200-16205400	Weak transcription	Dnd41	blood
30	chr17:16181600-16188000	Weak transcription	Fetal Thymus	thymus
31	chr17:16181800-16189400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr17:16182000-16189200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr17:16182200-16189000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr17:16182200-16189000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr17:16182400-16186600	Weak transcription	Fetal Intestine Small	intestine
36	chr17:16182600-16188000	Weak transcription	Primary B cells from cord blood	blood
37	chr17:16182600-16188400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr17:16182600-16188400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr17:16182600-16188800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr17:16182600-16189000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr17:16182600-16189000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr17:16182600-16189000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr17:16182600-16189200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr17:16182800-16189000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr17:16182800-16189000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr17:16183200-16188400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr17:16183200-16188800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr17:16183400-16188400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr17:16183400-16189000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr17:16183400-16189000	Weak transcription	Fetal Muscle Trunk	muscle

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