Variant report

Variant	rs17236194
Chromosome Location	chr15:59002755-59002756
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59002723..59004883-chr15:59065189..59066915,2	K562	blood:
2	chr15:58994779..58996470-chr15:59002182..59005147,2	K562	blood:

Variant related genes	Relation type
ENSG00000199730	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11071391	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11071393	0.94[CEU][hapmap];0.93[TSI][hapmap]
rs11071397	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs12437457	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap]
rs12437952	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12437998	0.85[AMR][1000 genomes]
rs12438487	0.88[CEU][hapmap]
rs12439231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12439632	0.87[CEU][hapmap];0.94[CHB][hapmap]
rs12440267	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12441313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12441912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12442451	1.00[CEU][hapmap]
rs12591310	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs12592332	0.94[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap]
rs12594742	0.88[CEU][hapmap]
rs12708455	0.94[CEU][hapmap]
rs12900343	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12901989	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs12905110	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906705	0.94[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs12906714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12907237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12908165	0.80[CEU][hapmap]
rs12908261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12912286	0.94[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs12912327	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12913383	0.83[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs12913969	0.81[CEU][hapmap]
rs12917500	0.83[AMR][1000 genomes]
rs12917577	0.94[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs1426652	0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs1551445	0.88[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs16940587	0.94[CEU][hapmap]
rs16940589	0.94[CEU][hapmap]
rs16940647	0.88[CEU][hapmap]
rs16940651	0.88[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs17301864	0.82[CEU][hapmap]
rs17301954	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2052805	0.94[CEU][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes]
rs2305421	0.94[CEU][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs2414608	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28455654	0.93[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes]
rs28470809	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28489732	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28536555	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28549001	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28818840	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35956992	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6074	1.00[ASW][hapmap];0.82[CEU][hapmap]
rs6494030	0.88[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs6494031	0.94[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs6494033	0.88[CEU][hapmap]
rs6494034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6494038	0.94[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs7163733	0.94[CEU][hapmap]
rs7163939	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7165035	0.88[CEU][hapmap]
rs7165402	0.88[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs7166076	0.88[CEU][hapmap]
rs7166325	0.88[CEU][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap]
rs7167528	0.94[CEU][hapmap];0.83[AMR][1000 genomes]
rs7169205	0.88[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs7170314	0.88[CEU][hapmap]
rs7174386	0.87[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs7174414	0.93[CEU][hapmap]
rs8029301	0.94[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs8029805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036005	0.94[CEU][hapmap]
rs8036448	0.82[EUR][1000 genomes]
rs8039791	0.83[CEU][hapmap];0.84[GIH][hapmap]
rs871804	1.00[ASW][hapmap]
rs9302203	0.88[CEU][hapmap]
rs9635351	0.94[CEU][hapmap]
rs9920720	0.88[CEU][hapmap]
rs9921024	0.94[CEU][hapmap]

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	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17236194	PIGB	cis	cerebellum	SCAN
rs17236194	RNF111	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58977200-59004400	Weak transcription	Ovary	ovary
2	chr15:58977200-59007800	Weak transcription	HepG2	liver
3	chr15:58977200-59039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:58982400-59005000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:58982600-59008000	Weak transcription	Fetal Brain Male	brain
6	chr15:58983200-59016600	Weak transcription	Small Intestine	intestine
7	chr15:58985200-59005000	Weak transcription	HSMMtube	muscle
8	chr15:58986600-59016600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr15:58987400-59012000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:58987600-59005000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:58987600-59007800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:58989800-59016800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:58990000-59004800	Weak transcription	Pancreas	Pancrea
14	chr15:58990000-59005000	Weak transcription	Spleen	Spleen
15	chr15:58990000-59005200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:58990000-59023400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:58991600-59005200	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:58991800-59005000	Weak transcription	Liver	Liver
19	chr15:58991800-59005000	Weak transcription	Fetal Kidney	kidney
20	chr15:58991800-59005000	Weak transcription	HMEC	breast
21	chr15:58991800-59012200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:58992000-59005000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr15:58992000-59009000	Weak transcription	Placenta	Placenta
24	chr15:58992000-59010800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:58992000-59015800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr15:58992000-59023000	Weak transcription	Esophagus	oesophagus
27	chr15:58992000-59023800	Weak transcription	Aorta	Aorta
28	chr15:58992200-59004400	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:58992200-59008600	Weak transcription	Fetal Lung	lung
30	chr15:58992400-59004600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr15:58992400-59005000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:58992400-59005200	Weak transcription	NHEK	skin
33	chr15:58992400-59005600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:58992400-59011600	Weak transcription	HUVEC	blood vessel
35	chr15:58992400-59012000	Weak transcription	Brain Anterior Caudate	brain
36	chr15:58992600-59005000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:58992600-59016600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:58992600-59021000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr15:58992800-59007200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:58992800-59008400	Weak transcription	A549	lung
41	chr15:58993200-59005000	Weak transcription	Thymus	Thymus
42	chr15:58993200-59010200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr15:58993200-59010800	Weak transcription	K562	blood
44	chr15:58993400-59010600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:58994000-59005000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr15:58994200-59005000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr15:58994400-59003000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:58994400-59004800	Weak transcription	Fetal Intestine Large	intestine
49	chr15:58994400-59012400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:58994400-59016400	Weak transcription	Adipose Nuclei	Adipose

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