Variant report

Variant	rs11058226
Chromosome Location	chr12:122938958-122938959
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	chr12:122905298..122908189-chr12:122936931..122940541,4	K562	blood:
2	chr12:122934144..122936687-chr12:122938638..122940695,2	K562	blood:

Variant related genes	Relation type
ENSG00000130779	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10161534	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10734915	1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10734918	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10734924	1.00[JPT][hapmap]
rs10744192	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10744208	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10744209	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10744210	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10744211	0.94[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10744217	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10744218	0.81[AFR][1000 genomes]
rs10744220	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10744287	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10773075	0.89[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.89[TSI][hapmap]
rs10773088	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10773103	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10773104	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10773152	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs10773167	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10773172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773176	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10773178	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10773208	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10773394	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10846664	0.94[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs10846688	0.92[CHB][hapmap]
rs10846699	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10846746	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10846764	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10846792	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10846830	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10846912	0.84[YRI][hapmap];0.87[AFR][1000 genomes]
rs10846920	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10846921	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10846931	0.92[EUR][1000 genomes]
rs10846978	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs10847179	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10847242	1.00[JPT][hapmap]
rs10998	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11057786	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11057797	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11057882	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11058034	0.92[EUR][1000 genomes]
rs11058209	0.85[EUR][1000 genomes]
rs11058233	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11058251	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11058282	0.81[EUR][1000 genomes]
rs11058402	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11616082	0.89[EUR][1000 genomes]
rs11836188	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12369858	0.94[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs12372756	0.94[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs12423420	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425970	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12581249	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1473553	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1803290	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1818050	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1973463	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2062488	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs2341439	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28730465	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34129612	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3817011	0.94[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs4319547	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs4758643	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4758644	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4758645	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4758646	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4758648	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4758662	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4758666	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4997380	0.94[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs55834409	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6488933	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6488939	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6488951	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6488958	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6489002	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6489156	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs6489157	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs7135419	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7294559	0.94[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7301515	0.89[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs7307735	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs7314638	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7316114	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7397990	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7398014	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7952868	0.85[EUR][1000 genomes]
rs7954006	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7956480	0.89[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap]
rs7959238	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7964138	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7969429	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7974262	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7975747	0.94[CEU][hapmap];0.86[JPT][hapmap]
rs9705654	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9788145	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9988963	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	173 gene(s)	inside rSNPs	diseases
2	nsv973945	chr12:122923254-122958354	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11058226	B3GNT4	cis	cerebellum	SCAN
rs11058226	UGT2B17	trans	lymphoblastoid	seeQTL
rs11058226	LRRC43	cis	parietal	SCAN
rs11058226	GTF2H3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122922800-122960400	Weak transcription	Right Atrium	heart
2	chr12:122934800-122942800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:122935400-122943800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:122936600-122939200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr12:122936600-122939200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr12:122936600-122939800	Enhancers	Primary T cells fromperipheralblood	blood
7	chr12:122936800-122939000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:122936800-122939200	Enhancers	Primary T cells from cord blood	blood
9	chr12:122937000-122939000	Enhancers	Primary B cells from cord blood	blood
10	chr12:122937200-122939000	Enhancers	Primary B cells from peripheral blood	blood
11	chr12:122937200-122939000	Enhancers	Primary hematopoietic stem cells	blood
12	chr12:122937200-122939000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:122937200-122939000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:122937200-122939000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:122937200-122939200	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr12:122937200-122939600	Enhancers	Fetal Thymus	thymus
17	chr12:122937400-122939000	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr12:122937400-122939000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:122937400-122939000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:122937400-122939000	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr12:122937400-122939800	Enhancers	Duodenum Mucosa	Duodenum
22	chr12:122937600-122939000	Enhancers	Spleen	Spleen
23	chr12:122937800-122939200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr12:122937800-122939200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:122937800-122939200	Enhancers	Dnd41	blood
26	chr12:122937800-122939200	Enhancers	Hela-S3	cervix
27	chr12:122938000-122939000	Enhancers	Placenta	Placenta
28	chr12:122938200-122939000	Enhancers	Esophagus	oesophagus
29	chr12:122938400-122939000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:122938400-122939000	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr12:122938400-122939000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr12:122938400-122939400	Flanking Active TSS	HepG2	liver
33	chr12:122938400-122940200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr12:122938600-122939000	Enhancers	HMEC	breast
35	chr12:122938600-122939200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:122938600-122939200	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr12:122938600-122939400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:122938600-122939600	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr12:122938600-122939600	Enhancers	A549	lung
40	chr12:122938800-122939200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr12:122938800-122939400	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr12:122938800-122939600	Weak transcription	Small Intestine	intestine
43	chr12:122938800-122940400	Weak transcription	Fetal Intestine Large	intestine
44	chr12:122938800-122940800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr12:122938800-122942000	Weak transcription	GM12878-XiMat	blood
46	chr12:122938800-122942200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:122938800-122943400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr12:122938800-122943800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:122938800-122943800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:122938800-122957000	Weak transcription	Thymus	Thymus

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