Variant report

Variant	rs12948244
Chromosome Location	chr17:16178100-16178101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16171013..16172613-chr17:16176178..16178945,3	K562	blood:
2	chr17:16175952..16178833-chr17:16340980..16343574,2	K562	blood:
3	chr17:16175415..16178833-chr17:16340980..16343676,3	K562	blood:

Variant related genes	Relation type
ENSG00000175061	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10852834	0.83[EUR][1000 genomes]
rs11078337	0.82[EUR][1000 genomes]
rs11650956	0.83[EUR][1000 genomes]
rs11651578	0.83[CEU][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs11652044	0.82[EUR][1000 genomes]
rs11653500	0.87[EUR][1000 genomes]
rs11654658	0.85[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs11655325	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11655906	0.82[EUR][1000 genomes]
rs11655907	0.82[EUR][1000 genomes]
rs11656811	0.85[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs11868284	0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs12150285	0.81[EUR][1000 genomes]
rs12150564	0.81[EUR][1000 genomes]
rs12936529	0.83[EUR][1000 genomes]
rs12938394	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12938397	0.82[EUR][1000 genomes]
rs12938878	0.83[EUR][1000 genomes]
rs12939078	0.83[EUR][1000 genomes]
rs12945959	0.86[EUR][1000 genomes]
rs12946619	0.87[EUR][1000 genomes]
rs1476810	0.82[CHB][hapmap]
rs178785	0.83[EUR][1000 genomes]
rs178787	0.85[EUR][1000 genomes]
rs1963811	0.84[EUR][1000 genomes]
rs2014604	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074995	0.81[CEU][hapmap]
rs2109262	0.82[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs2324306	0.81[EUR][1000 genomes]
rs2324307	0.85[EUR][1000 genomes]
rs28516015	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3095171	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3112511	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3112513	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34331598	0.86[EUR][1000 genomes]
rs35565381	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3785621	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3785622	0.83[EUR][1000 genomes]
rs3785623	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3785625	0.83[CEU][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs3785626	0.82[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs4470185	0.86[EUR][1000 genomes]
rs4791665	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4792728	0.82[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs4792729	0.85[EUR][1000 genomes]
rs4792730	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4792731	0.85[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs4792735	0.82[EUR][1000 genomes]
rs56269147	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62072527	0.87[EUR][1000 genomes]
rs6502498	0.81[EUR][1000 genomes]
rs6502499	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7210990	0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs7219687	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223428	0.87[EUR][1000 genomes]
rs7224367	0.85[EUR][1000 genomes]
rs7225920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8073259	0.85[EUR][1000 genomes]
rs8074727	0.86[EUR][1000 genomes]
rs9303135	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9747114	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9890539	0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[EUR][1000 genomes]
rs9893005	0.81[EUR][1000 genomes]
rs9910148	0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs9914734	0.86[CEU][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs9944524	0.85[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv907719	chr17:16161036-16185122	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12948244	LOC125150	cis	lesional skin	skin_eQTL
rs12948244	ADORA2B	cis	Thyroid	GTEx
rs12948244	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs12948244	CENPV	cis	Artery Tibial	GTEx
rs12948244	ADORA2B	cis	Nerve Tibial	GTEx
rs12948244	ADORA2B	cis	Esophagus Muscularis	GTEx
rs12948244	LOC125150	cis	normal skin	skin_eQTL
rs12948244	ADORA2B	cis	Muscle Skeletal	GTEx
rs12948244	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs12948244	LOC125150	cis	uninvolved skin	skin_eQTL
rs12948244	ADORA2B	cis	Artery Tibial	GTEx
rs12948244	ZSWIM7	cis	Muscle Skeletal	GTEx
rs12948244	PRR6	cis	multi-tissue	Pritchard
rs12948244	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16157400-16185200	Weak transcription	Gastric	stomach
2	chr17:16159200-16178400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr17:16159400-16189200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr17:16159600-16188800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr17:16159600-16189000	Weak transcription	Brain Anterior Caudate	brain
6	chr17:16160000-16183000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr17:16160400-16188400	Weak transcription	Liver	Liver
8	chr17:16163400-16189200	Weak transcription	Left Ventricle	heart
9	chr17:16163600-16189200	Weak transcription	Pancreas	Pancrea
10	chr17:16164000-16180800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr17:16164000-16182400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr17:16164000-16182400	Weak transcription	Fetal Muscle Leg	muscle
13	chr17:16164000-16185000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr17:16164000-16189000	Weak transcription	Fetal Brain Female	brain
15	chr17:16164000-16189000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr17:16164200-16182200	Weak transcription	Fetal Stomach	stomach
17	chr17:16164600-16182200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr17:16166200-16205400	Weak transcription	Brain Hippocampus Middle	brain
19	chr17:16168600-16188800	Weak transcription	Fetal Intestine Large	intestine
20	chr17:16171000-16181600	Weak transcription	HepG2	liver
21	chr17:16171400-16188200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr17:16171400-16189000	Weak transcription	Spleen	Spleen
23	chr17:16171600-16182200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr17:16171600-16188200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr17:16172000-16180400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr17:16172000-16185200	Weak transcription	Lung	lung
27	chr17:16172600-16188200	Weak transcription	GM12878-XiMat	blood
28	chr17:16173000-16187800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr17:16173000-16188200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr17:16173200-16180400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr17:16173200-16183200	Weak transcription	Primary T cells from cord blood	blood
32	chr17:16173200-16185400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr17:16173200-16186800	Weak transcription	Fetal Lung	lung
34	chr17:16173200-16187800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr17:16173200-16188000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr17:16173400-16187800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr17:16173400-16187800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr17:16173400-16188200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr17:16173600-16185200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr17:16174800-16183000	Weak transcription	Ovary	ovary
41	chr17:16175000-16189000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr17:16175400-16180000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr17:16176200-16179800	Weak transcription	Fetal Intestine Small	intestine
44	chr17:16176200-16188800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr17:16176400-16178800	Enhancers	K562	blood
46	chr17:16177200-16184200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr17:16177400-16181400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr17:16177600-16181400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr17:16177600-16181400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr17:16177600-16183800	Weak transcription	NH-A	brain

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