Variant report

Variant	rs12591294
Chromosome Location	chr15:56525994-56525995
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	chr15:56523183..56527072-chr15:56528127..56530635,4	K562	blood:

Extended variants
information (count: 183 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:180)

rs_ID	r²[population]
rs1031077	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10518839	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10518842	0.93[ASN][1000 genomes]
rs10518843	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10851601	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10851603	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10851604	0.98[ASN][1000 genomes]
rs11071245	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11071246	0.81[ASN][1000 genomes]
rs11071252	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11071253	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11071254	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071255	0.98[ASN][1000 genomes]
rs11629674	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11629809	0.98[ASN][1000 genomes]
rs11630394	0.98[ASN][1000 genomes]
rs11631518	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11631910	0.98[ASN][1000 genomes]
rs11631915	0.94[ASN][1000 genomes]
rs11632023	0.95[ASN][1000 genomes]
rs11632081	0.98[ASN][1000 genomes]
rs11632087	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11632091	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11632394	0.98[ASN][1000 genomes]
rs11632619	0.98[ASN][1000 genomes]
rs11634404	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11634455	0.93[ASN][1000 genomes]
rs11634689	0.97[ASN][1000 genomes]
rs11636035	0.98[ASN][1000 genomes]
rs11636040	0.90[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs11637507	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11637515	0.98[ASN][1000 genomes]
rs11637789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11637998	0.98[ASN][1000 genomes]
rs11638709	0.93[ASN][1000 genomes]
rs12437864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12439682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12439907	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12440142	0.94[EUR][1000 genomes]
rs12442539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12443042	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs12443118	0.84[ASN][1000 genomes]
rs12443429	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12591093	0.98[ASN][1000 genomes]
rs12591151	0.82[ASN][1000 genomes]
rs12591236	0.92[ASN][1000 genomes]
rs12591270	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12591980	0.93[ASN][1000 genomes]
rs12592096	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12592130	0.95[ASN][1000 genomes]
rs12592449	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12592881	0.96[ASN][1000 genomes]
rs12592899	0.97[ASN][1000 genomes]
rs12593096	0.98[ASN][1000 genomes]
rs12593439	0.96[ASN][1000 genomes]
rs12593569	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12593713	0.98[ASN][1000 genomes]
rs12593752	0.93[ASN][1000 genomes]
rs12594038	0.96[ASN][1000 genomes]
rs12594103	0.89[ASN][1000 genomes]
rs12594121	0.98[ASN][1000 genomes]
rs12594245	0.93[ASN][1000 genomes]
rs12594860	0.93[ASN][1000 genomes]
rs12594908	0.92[ASN][1000 genomes]
rs12594941	0.95[CHB][hapmap]
rs12595072	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12595323	0.98[ASN][1000 genomes]
rs12595366	0.95[ASN][1000 genomes]
rs12595428	0.97[ASN][1000 genomes]
rs12595490	0.94[ASN][1000 genomes]
rs12595496	0.94[ASN][1000 genomes]
rs12595557	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs12595649	0.93[ASN][1000 genomes]
rs12595690	0.92[ASN][1000 genomes]
rs12595840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1402173	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs1550586	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs16976734	0.88[GIH][hapmap]
rs16976760	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16976788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16976792	0.93[ASN][1000 genomes]
rs16976801	0.93[ASN][1000 genomes]
rs16976810	0.93[ASN][1000 genomes]
rs16976821	0.93[ASN][1000 genomes]
rs16976826	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976831	0.98[ASN][1000 genomes]
rs16976832	0.98[ASN][1000 genomes]
rs16976847	0.95[CHB][hapmap]
rs17841131	0.93[ASN][1000 genomes]
rs1867089	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1879344	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1879345	0.93[ASN][1000 genomes]
rs1879347	1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1879348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1879349	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2162216	0.95[CHB][hapmap]
rs2414465	0.98[ASN][1000 genomes]
rs2414467	0.98[ASN][1000 genomes]
rs2414468	0.98[ASN][1000 genomes]
rs2414471	0.97[ASN][1000 genomes]
rs2414472	0.96[ASN][1000 genomes]
rs2682045	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2718930	0.94[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2899596	0.93[ASN][1000 genomes]
rs2899597	0.93[ASN][1000 genomes]
rs34401800	0.95[ASN][1000 genomes]
rs35371323	0.80[ASN][1000 genomes]
rs35607436	0.98[ASN][1000 genomes]
rs4142479	0.89[CHB][hapmap]
rs4363812	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55942364	0.98[ASN][1000 genomes]
rs55957636	0.98[ASN][1000 genomes]
rs56083605	0.98[ASN][1000 genomes]
rs56156930	0.93[ASN][1000 genomes]
rs56215018	0.98[ASN][1000 genomes]
rs56305704	0.84[ASN][1000 genomes]
rs56323443	0.82[ASN][1000 genomes]
rs56398703	0.97[ASN][1000 genomes]
rs58084889	0.88[ASN][1000 genomes]
rs58265497	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58934221	0.98[ASN][1000 genomes]
rs59025920	0.84[ASN][1000 genomes]
rs59230019	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60210425	0.93[ASN][1000 genomes]
rs60417530	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61270078	0.97[ASN][1000 genomes]
rs61466134	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs68127612	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7177904	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs72736479	0.83[ASN][1000 genomes]
rs72736495	0.84[ASN][1000 genomes]
rs72736498	0.84[ASN][1000 genomes]
rs72738604	0.88[ASN][1000 genomes]
rs72738605	0.86[ASN][1000 genomes]
rs72738607	0.88[ASN][1000 genomes]
rs72738608	0.87[ASN][1000 genomes]
rs72738615	0.92[ASN][1000 genomes]
rs72738616	0.95[ASN][1000 genomes]
rs72738618	0.95[ASN][1000 genomes]
rs72738620	0.92[ASN][1000 genomes]
rs72738631	0.95[ASN][1000 genomes]
rs72738636	0.94[ASN][1000 genomes]
rs72738638	0.93[ASN][1000 genomes]
rs72738646	0.92[ASN][1000 genomes]
rs72738648	0.93[ASN][1000 genomes]
rs72738654	0.93[ASN][1000 genomes]
rs72738656	0.93[ASN][1000 genomes]
rs72738658	0.93[ASN][1000 genomes]
rs72738659	0.93[ASN][1000 genomes]
rs72738660	0.93[ASN][1000 genomes]
rs72738662	0.93[ASN][1000 genomes]
rs72738664	0.93[ASN][1000 genomes]
rs72738666	0.93[ASN][1000 genomes]
rs72738667	0.93[ASN][1000 genomes]
rs72738668	0.93[ASN][1000 genomes]
rs72738674	0.98[ASN][1000 genomes]
rs72738675	0.98[ASN][1000 genomes]
rs72738676	0.98[ASN][1000 genomes]
rs72738679	0.98[ASN][1000 genomes]
rs72738680	0.98[ASN][1000 genomes]
rs72738682	0.98[ASN][1000 genomes]
rs72738683	0.98[ASN][1000 genomes]
rs72738684	0.98[ASN][1000 genomes]
rs72738685	0.98[ASN][1000 genomes]
rs72738686	0.98[ASN][1000 genomes]
rs72738694	0.98[ASN][1000 genomes]
rs72738696	0.98[ASN][1000 genomes]
rs72738697	0.98[ASN][1000 genomes]
rs72738701	0.96[ASN][1000 genomes]
rs72740503	0.96[ASN][1000 genomes]
rs72740505	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72740506	0.95[ASN][1000 genomes]
rs72740508	0.97[ASN][1000 genomes]
rs72740509	0.97[ASN][1000 genomes]
rs72740514	0.90[ASN][1000 genomes]
rs748970	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs764014	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs8023554	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs8027386	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030605	0.97[ASN][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	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv569547	chr15:56504598-56572176	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2760380	chr15:56510123-56529955	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12591294	SCG3	cis	parietal	SCAN
rs12591294	UNC13C	cis	parietal	SCAN
rs12591294	MNS1	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56508000-56534400	Weak transcription	Fetal Heart	heart
2	chr15:56509000-56533600	Weak transcription	Osteobl	bone
3	chr15:56510600-56528600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr15:56513800-56530200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
5	chr15:56514000-56535000	Weak transcription	Pancreas	Pancrea
6	chr15:56514600-56532400	Weak transcription	HSMMtube	muscle
7	chr15:56514800-56534800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:56515800-56529200	Weak transcription	Colon Smooth Muscle	Colon
9	chr15:56518600-56527400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:56519400-56528400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr15:56520000-56527200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:56520200-56530200	ZNF genes & repeats	Dnd41	blood
13	chr15:56520400-56526000	ZNF genes & repeats	Brain Germinal Matrix	brain
14	chr15:56520400-56526600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr15:56520400-56526800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:56520400-56527400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr15:56520600-56526400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:56520800-56526200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:56520800-56526600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
20	chr15:56521000-56526000	ZNF genes & repeats	Fetal Intestine Small	intestine
21	chr15:56521000-56526200	ZNF genes & repeats	Primary B cells from cord blood	blood
22	chr15:56521200-56527000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:56521200-56528000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:56521400-56526200	ZNF genes & repeats	Fetal Lung	lung
25	chr15:56521400-56526800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
26	chr15:56521400-56532000	ZNF genes & repeats	GM12878-XiMat	blood
27	chr15:56521600-56526000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
28	chr15:56521800-56526800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
29	chr15:56521800-56527200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:56522000-56526800	ZNF genes & repeats	A549	lung
31	chr15:56522000-56527400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
32	chr15:56522200-56526200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
33	chr15:56522200-56526200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
34	chr15:56522200-56527400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
35	chr15:56522400-56526200	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr15:56522400-56526600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
37	chr15:56522800-56526000	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
38	chr15:56522800-56526200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
39	chr15:56522800-56533600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr15:56523000-56526000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
41	chr15:56523200-56526200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
42	chr15:56523200-56526200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:56523200-56526600	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
44	chr15:56523800-56526000	ZNF genes & repeats	Liver	Liver
45	chr15:56523800-56526000	ZNF genes & repeats	Brain Angular Gyrus	brain
46	chr15:56523800-56526400	ZNF genes & repeats	HepG2	liver
47	chr15:56524400-56526400	ZNF genes & repeats	Primary T cells from cord blood	blood
48	chr15:56524600-56526000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:56524600-56526400	Weak transcription	HUVEC	blood vessel
50	chr15:56524600-56526800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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