Variant report

Variant	rs12186259
Chromosome Location	chr4:120152039-120152040
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:120136237..120140737-chr4:120147652..120152174,4	MCF-7	breast:
2	chr4:120146321..120148170-chr4:120150599..120152803,2	K562	blood:
3	chr4:120151295..120153749-chr4:120154352..120157062,2	K562	blood:
4	chr4:120132760..120135331-chr4:120151065..120152751,2	MCF-7	breast:
5	chr4:120151994..120154554-chr4:120157115..120160600,3	K562	blood:
6	chr4:120132067..120136254-chr4:120151434..120157051,7	K562	blood:
7	chr4:120132397..120137812-chr4:120151434..120157051,7	K562	blood:

Variant related genes	Relation type
ENSG00000178636	Chromatin interaction
ENSG00000145390	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10006304	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10006877	0.86[JPT][hapmap]
rs10010696	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10013032	0.83[EUR][1000 genomes]
rs10022262	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10022508	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10029750	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10031033	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1011054	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10213342	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1052633	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11098489	0.81[ASN][1000 genomes]
rs11098496	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11098498	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs11098499	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11726229	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11729897	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11729978	0.80[ASN][1000 genomes]
rs11730138	0.81[ASN][1000 genomes]
rs11731008	0.81[ASN][1000 genomes]
rs11731571	0.86[JPT][hapmap]
rs11732621	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11733525	0.81[ASN][1000 genomes]
rs11734519	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11931312	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11944880	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12499598	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12501610	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12502503	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12506395	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12508316	0.81[ASN][1000 genomes]
rs12509054	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12512517	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13113112	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13114751	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13116504	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13123591	0.89[EUR][1000 genomes]
rs13126596	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13129661	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13133044	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13138782	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13139045	0.84[CEU][hapmap]
rs13435802	0.82[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1397608	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1511015	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1511018	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1511019	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1546502	0.86[JPT][hapmap]
rs1546505	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs1551	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17839089	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs2203039	0.81[EUR][1000 genomes]
rs28374891	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28419773	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28452522	0.82[EUR][1000 genomes]
rs28555550	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34585914	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34616304	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34630083	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35197422	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35271032	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35434465	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35643470	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35916640	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3749591	0.94[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4145951	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4334737	0.81[ASN][1000 genomes]
rs4833612	0.83[EUR][1000 genomes]
rs56122576	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56386062	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6534130	0.81[EUR][1000 genomes]
rs67073020	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68128210	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6814412	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6815725	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6822498	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6822808	0.90[JPT][hapmap]
rs6826823	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6832670	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6837898	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6838674	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6843509	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs6845702	0.85[EUR][1000 genomes]
rs6849889	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6851169	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7441137	0.81[EUR][1000 genomes]
rs7659194	0.94[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7661020	0.89[EUR][1000 genomes]
rs7684942	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7685268	0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7696877	0.81[ASN][1000 genomes]
rs951570	0.83[EUR][1000 genomes]
rs9884728	0.81[EUR][1000 genomes]
rs9995277	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs9996382	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	esv2763386	chr4:120143861-120186968	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv966480	chr4:120144708-120160847	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12186259	RP11-33B1.1	cis	Whole Blood	GTEx
rs12186259	RP11-33B1.1	cis	lung	GTEx
rs12186259	RP11-384K6.6	cis	Whole Blood	GTEx
rs12186259	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs12186259	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120134800-120170000	Weak transcription	Colon Smooth Muscle	Colon
2	chr4:120135000-120154800	Weak transcription	Primary B cells from cord blood	blood
3	chr4:120135000-120170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:120135000-120195800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:120135200-120155000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:120135200-120155000	Weak transcription	Small Intestine	intestine
7	chr4:120135200-120163600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:120135200-120176200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:120135200-120176200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr4:120135400-120159000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr4:120135400-120194600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:120135600-120155000	Weak transcription	K562	blood
13	chr4:120135600-120173800	Weak transcription	Brain Anterior Caudate	brain
14	chr4:120136200-120154400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
16	chr4:120136400-120155000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:120136400-120155000	Weak transcription	Stomach Mucosa	stomach
18	chr4:120136400-120156400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:120137400-120155000	Weak transcription	Right Atrium	heart
20	chr4:120137600-120154600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr4:120138800-120155000	Weak transcription	Fetal Thymus	thymus
22	chr4:120139400-120165800	Weak transcription	Fetal Kidney	kidney
23	chr4:120139600-120153600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:120140000-120155000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:120140200-120154800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr4:120140200-120154800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr4:120140600-120167400	Weak transcription	Colonic Mucosa	Colon
28	chr4:120140800-120152800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr4:120140800-120154600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr4:120140800-120154800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:120140800-120158800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:120141000-120153800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr4:120141000-120154600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr4:120141000-120154600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:120141000-120154800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:120141000-120158800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr4:120141000-120192400	Weak transcription	Hela-S3	cervix
38	chr4:120142400-120155000	Weak transcription	Ovary	ovary
39	chr4:120143000-120155000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr4:120143000-120155000	Weak transcription	HSMMtube	muscle
41	chr4:120143000-120156400	Weak transcription	Fetal Stomach	stomach
42	chr4:120143000-120156600	Weak transcription	Fetal Intestine Small	intestine
43	chr4:120143000-120167200	Weak transcription	Placenta	Placenta
44	chr4:120143000-120176200	Weak transcription	Esophagus	oesophagus
45	chr4:120143200-120155000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:120143800-120153000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:120143800-120153400	Weak transcription	HMEC	breast
48	chr4:120143800-120153800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr4:120143800-120156400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr4:120143800-120167000	Weak transcription	Fetal Intestine Large	intestine

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