Variant report

Variant	rs12655223
Chromosome Location	chr5:126237059-126237060
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	chr5:126231811..126233639-chr5:126236642..126239231,2	K562	blood:

Extended variants
information (count: 188 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:183)

rs_ID	r²[population]
rs10040840	0.82[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10519919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10519922	0.82[EUR][1000 genomes]
rs10519923	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12518420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12651864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12652390	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12652417	0.82[EUR][1000 genomes]
rs12653000	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12653290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12653444	0.82[EUR][1000 genomes]
rs12654717	0.82[EUR][1000 genomes]
rs12654725	0.82[EUR][1000 genomes]
rs12654808	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655006	0.85[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs12655199	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12655258	0.85[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs12655319	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12655435	0.82[EUR][1000 genomes]
rs12655605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12655726	0.82[EUR][1000 genomes]
rs12655928	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12655991	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12656236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12656537	0.85[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12656837	0.85[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs12658138	0.85[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs12658174	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658599	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12658608	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12658816	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12658821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12658822	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12659476	0.82[EUR][1000 genomes]
rs12659607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12659614	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12659633	0.82[EUR][1000 genomes]
rs17165192	0.82[EUR][1000 genomes]
rs17165194	0.82[EUR][1000 genomes]
rs17165211	0.82[EUR][1000 genomes]
rs17165213	1.00[TSI][hapmap]
rs17165228	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17165234	0.85[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs17165239	0.82[EUR][1000 genomes]
rs17165248	0.82[GIH][hapmap]
rs17165249	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17165251	0.82[CHD][hapmap];0.85[GIH][hapmap]
rs34416835	0.82[EUR][1000 genomes]
rs34738240	0.82[EUR][1000 genomes]
rs35566904	0.82[EUR][1000 genomes]
rs35627668	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs36091921	0.82[EUR][1000 genomes]
rs3805737	1.00[MEX][hapmap]
rs3812061	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4141169	0.82[EUR][1000 genomes]
rs4141170	0.82[GIH][hapmap]
rs55792418	0.82[EUR][1000 genomes]
rs55802546	0.82[EUR][1000 genomes]
rs56094173	0.82[EUR][1000 genomes]
rs56124224	0.82[EUR][1000 genomes]
rs56272610	0.82[EUR][1000 genomes]
rs56688052	0.82[EUR][1000 genomes]
rs56689722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56786115	0.82[EUR][1000 genomes]
rs57031083	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57032367	0.82[EUR][1000 genomes]
rs57052202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57081850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57113926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57485054	1.00[EUR][1000 genomes]
rs57627287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57700815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57833976	0.82[EUR][1000 genomes]
rs57906418	0.95[ASN][1000 genomes]
rs57915728	0.82[EUR][1000 genomes]
rs58164143	0.82[EUR][1000 genomes]
rs58262537	0.82[EUR][1000 genomes]
rs58527455	0.82[EUR][1000 genomes]
rs58646561	0.82[EUR][1000 genomes]
rs58838495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58894799	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59459356	0.82[EUR][1000 genomes]
rs59489123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59643871	0.82[EUR][1000 genomes]
rs59676931	0.82[EUR][1000 genomes]
rs59814275	0.82[EUR][1000 genomes]
rs60045571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60138815	0.82[EUR][1000 genomes]
rs60244211	0.95[ASN][1000 genomes]
rs60615137	0.82[EUR][1000 genomes]
rs60636815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60781824	0.82[EUR][1000 genomes]
rs60889784	0.82[EUR][1000 genomes]
rs61031864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61258380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61279308	0.82[EUR][1000 genomes]
rs61463824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61496590	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61647801	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61653213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61685918	0.82[EUR][1000 genomes]
rs6595747	0.82[GIH][hapmap]
rs6860581	0.82[GIH][hapmap]
rs6862462	0.82[EUR][1000 genomes]
rs6864607	0.85[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6872893	0.82[EUR][1000 genomes]
rs6877692	0.85[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs6882025	0.82[EUR][1000 genomes]
rs6883181	0.82[EUR][1000 genomes]
rs6888532	0.82[EUR][1000 genomes]
rs6893763	0.82[EUR][1000 genomes]
rs6899030	0.82[EUR][1000 genomes]
rs72505648	1.00[EUR][1000 genomes]
rs73335426	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73335444	1.00[EUR][1000 genomes]
rs73335447	1.00[EUR][1000 genomes]
rs73335461	1.00[EUR][1000 genomes]
rs73335474	1.00[EUR][1000 genomes]
rs73335490	0.82[EUR][1000 genomes]
rs73335494	0.82[EUR][1000 genomes]
rs73335498	0.82[EUR][1000 genomes]
rs73335501	0.82[EUR][1000 genomes]
rs73337229	0.82[EUR][1000 genomes]
rs73337233	0.82[EUR][1000 genomes]
rs73337299	0.82[EUR][1000 genomes]
rs73783476	1.00[EUR][1000 genomes]
rs73783496	0.82[EUR][1000 genomes]
rs73783501	0.82[EUR][1000 genomes]
rs73783503	0.82[EUR][1000 genomes]
rs73783504	0.82[EUR][1000 genomes]
rs73783506	0.82[EUR][1000 genomes]
rs73783507	0.82[EUR][1000 genomes]
rs73786207	0.82[EUR][1000 genomes]
rs73786209	0.82[EUR][1000 genomes]
rs73786212	0.82[EUR][1000 genomes]
rs73786239	0.82[EUR][1000 genomes]
rs73786240	0.82[EUR][1000 genomes]
rs73786241	0.82[EUR][1000 genomes]
rs73786242	0.82[EUR][1000 genomes]
rs73786244	0.82[EUR][1000 genomes]
rs73786246	0.82[EUR][1000 genomes]
rs73786247	0.82[EUR][1000 genomes]
rs73786249	0.82[EUR][1000 genomes]
rs73786250	0.82[EUR][1000 genomes]
rs73786251	0.82[EUR][1000 genomes]
rs73786252	0.82[EUR][1000 genomes]
rs73786253	0.82[EUR][1000 genomes]
rs73786255	0.82[EUR][1000 genomes]
rs73786259	0.82[EUR][1000 genomes]
rs73786260	0.82[EUR][1000 genomes]
rs73786261	0.82[EUR][1000 genomes]
rs73786262	0.82[EUR][1000 genomes]
rs73786264	0.82[EUR][1000 genomes]
rs73786265	0.82[EUR][1000 genomes]
rs73786266	0.82[EUR][1000 genomes]
rs73786268	0.82[EUR][1000 genomes]
rs73786269	0.82[EUR][1000 genomes]
rs73786270	0.82[EUR][1000 genomes]
rs73786271	0.82[EUR][1000 genomes]
rs73786272	0.82[EUR][1000 genomes]
rs73786276	0.82[EUR][1000 genomes]
rs73786277	0.82[EUR][1000 genomes]
rs73786278	0.82[EUR][1000 genomes]
rs73786280	0.82[EUR][1000 genomes]
rs73786281	0.82[EUR][1000 genomes]
rs73786282	0.82[EUR][1000 genomes]
rs73786283	0.82[EUR][1000 genomes]
rs73786284	0.82[EUR][1000 genomes]
rs73786285	0.82[EUR][1000 genomes]
rs73786287	0.82[EUR][1000 genomes]
rs73786288	0.82[EUR][1000 genomes]
rs73786290	0.82[EUR][1000 genomes]
rs73786294	0.82[EUR][1000 genomes]
rs73786295	0.82[EUR][1000 genomes]
rs73786298	0.82[EUR][1000 genomes]
rs73787403	0.82[EUR][1000 genomes]
rs73787404	0.82[EUR][1000 genomes]
rs73787406	0.82[EUR][1000 genomes]
rs7701976	0.96[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7709865	0.82[GIH][hapmap]
rs7715377	1.00[EUR][1000 genomes]
rs7727719	1.00[EUR][1000 genomes]
rs9918233	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949054	chr5:125918148-126254480	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv534292	chr5:125993451-126259315	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1024265	chr5:126213004-126691163	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv869897	chr5:126224358-126445210	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv969207	chr5:126232397-126237806	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12655223	PTH2	trans	lymphoblastoid	seeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126201800-126253400	Weak transcription	A549	lung
2	chr5:126205200-126245600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr5:126205400-126245600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:126205600-126238200	Weak transcription	Primary T cells from cord blood	blood
5	chr5:126214200-126237400	Weak transcription	Fetal Brain Female	brain
6	chr5:126214200-126238600	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:126214200-126238600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:126214200-126245400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr5:126214600-126245200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:126214600-126250400	Weak transcription	Pancreas	Pancrea
11	chr5:126214800-126255200	Weak transcription	Psoas Muscle	Psoas
12	chr5:126215400-126245000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:126220400-126238400	Weak transcription	Ovary	ovary
14	chr5:126220600-126238400	Weak transcription	Left Ventricle	heart
15	chr5:126220800-126237600	Weak transcription	Right Ventricle	heart
16	chr5:126220800-126245400	Weak transcription	HUVEC	blood vessel
17	chr5:126224000-126238400	Weak transcription	K562	blood
18	chr5:126226600-126237200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:126229600-126253600	Weak transcription	Brain Anterior Caudate	brain
20	chr5:126229800-126245800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr5:126230200-126238200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:126230200-126238400	Weak transcription	Lung	lung
23	chr5:126231200-126254000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:126231400-126245800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr5:126232400-126237200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr5:126232400-126237200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr5:126232400-126240000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:126232400-126245800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:126232600-126237200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr5:126232600-126237200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr5:126232600-126245400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr5:126232600-126245800	Weak transcription	Fetal Kidney	kidney
33	chr5:126233800-126256000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr5:126234000-126239200	Strong transcription	Primary B cells from cord blood	blood
35	chr5:126234600-126237200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:126234800-126238000	Weak transcription	HSMMtube	muscle
37	chr5:126236000-126239000	Enhancers	Fetal Brain Male	brain
38	chr5:126236000-126239200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:126236800-126237200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:126237000-126237600	Enhancers	H1 Cell Line	embryonic stem cell
41	chr5:126237000-126237600	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr5:126237000-126237800	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr5:126237000-126237800	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr5:126237000-126239200	Strong transcription	HSMM	muscle
45	chr5:126237000-126254000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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