Variant report

Variant	rs11204665
Chromosome Location	chr1:150536349-150536350
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MEF2A	chr1:150535067-150536354	GM12878	blood:	n/a	n/a
2	NFIC	chr1:150533611-150536549	GM12878	blood:	n/a	n/a
3	STAT3	chr1:150533488-150536437	MCF10A-Er-Src	breast:	n/a	chr1:150534049-150534061 chr1:150534647-150534656 chr1:150534644-150534658 chr1:150534645-150534656 chr1:150536224-150536232 chr1:150535410-150535422 chr1:150535415-150535427 chr1:150534646-150534655
4	POLR2A	chr1:150533330-150537703	GM12878	blood:	n/a	n/a
5	BCLAF1	chr1:150534968-150536352	GM12878	blood:	n/a	chr1:150535491-150535500 chr1:150535915-150535924
6	POLR2A	chr1:150536148-150536523	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr1:150533480-150536718	GM18951	blood:	n/a	n/a
8	SMC3	chr1:150535104-150536692	GM12878	blood:	n/a	n/a
9	MTA3	chr1:150534822-150536446	GM12878	blood:	n/a	n/a
10	STAT1	chr1:150533469-150536463	GM12878	blood:	n/a	chr1:150534049-150534061 chr1:150534647-150534656 chr1:150534644-150534658 chr1:150536224-150536232 chr1:150534645-150534656 chr1:150535410-150535422 chr1:150535415-150535427 chr1:150534646-150534655
11	CEBPB	chr1:150534886-150536454	GM12878	blood:	n/a	n/a
12	RELA	chr1:150534711-150536374	GM18526	blood:	n/a	n/a
13	POLR2A	chr1:150527732-150552686	MCF10A-Er-Src	breast:	n/a	n/a
14	BCLAF1	chr1:150533289-150536417	GM12878	blood:	n/a	chr1:150535491-150535500 chr1:150535915-150535924
15	POLR2A	chr1:150530622-150553130	IMR90	lung:	n/a	n/a
16	POLR2A	chr1:150533436-150537004	GM18505	blood:	n/a	n/a
17	RELA	chr1:150533391-150536483	GM18951	blood:	n/a	chr1:150534475-150534484 chr1:150534475-150534484
18	POLR2A	chr1:150533448-150536662	GM18526	blood:	n/a	n/a
19	FOXA1	chr1:150535903-150536470	T-47D	breast:	n/a	n/a
20	POLR2A	chr1:150532058-150538177	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr1:150536143-150536646	Hela-S3	cervix:	n/a	n/a
22	SP1	chr1:150536041-150536878	A549	lung:	n/a	n/a
23	EP300	chr1:150533317-150536683	SK-N-SH	brain:	n/a	chr1:150535526-150535542 chr1:150536506-150536520
24	POLR2A	chr1:150530539-150552850	MCF10A-Er-Src	breast:	n/a	n/a
25	MAZ	chr1:150533410-150536382	GM12878	blood:	n/a	n/a
26	RELA	chr1:150533446-150536616	GM19193	blood:	n/a	chr1:150534475-150534484 chr1:150534475-150534484
27	POLR2A	chr1:150536208-150536493	GM12878	blood:	n/a	n/a
28	STAT1	chr1:150533376-150536456	Hela-S3	cervix:	n/a	chr1:150534049-150534061 chr1:150534647-150534656 chr1:150534644-150534658 chr1:150536224-150536232 chr1:150534645-150534656 chr1:150535410-150535422 chr1:150535415-150535427 chr1:150534646-150534655
29	POLR2A	chr1:150536174-150536707	Hela-S3	cervix:	n/a	n/a
30	RCOR1	chr1:150534440-150536674	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:150533429-150536510	GM19193	blood:	n/a	n/a
32	STAT3	chr1:150534407-150536521	GM12878	blood:	n/a	chr1:150534647-150534656 chr1:150534644-150534658 chr1:150534645-150534656 chr1:150536224-150536232 chr1:150535410-150535422 chr1:150535415-150535427 chr1:150534646-150534655
33	RFX5	chr1:150532907-150537239	IMR90	lung:	n/a	chr1:150534721-150534730 chr1:150534717-150534732
34	POLR2A	chr1:150536233-150536496	A549	lung:	n/a	n/a
35	TBL1XR1	chr1:150533436-150536583	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:150536096-150536439	ECC-1	luminal epithelium:	n/a	n/a
37	BHLHE40	chr1:150533392-150536444	GM12878	blood:	n/a	n/a
38	ATF2	chr1:150534245-150536500	GM12878	blood:	n/a	chr1:150534431-150534442
39	RELA	chr1:150533402-150536718	GM12891	blood:	n/a	chr1:150534475-150534484 chr1:150534475-150534484
40	FOXM1	chr1:150533239-150536396	GM12878	blood:	n/a	n/a
41	CHD2	chr1:150533444-150536522	GM12878	blood:	n/a	n/a
42	STAT5A	chr1:150533330-150536898	GM12878	blood:	n/a	chr1:150534049-150534061 chr1:150534647-150534656 chr1:150534644-150534658 chr1:150536511-150536522 chr1:150536224-150536232 chr1:150536640-150536652 chr1:150535410-150535422 chr1:150535415-150535427 chr1:150534646-150534655
43	RUNX3	chr1:150533355-150536655	GM12878	blood:	n/a	chr1:150535341-150535350 chr1:150535341-150535350
44	NR3C1	chr1:150536232-150536839	A549	lung:	n/a	chr1:150536552-150536566
45	POLR2A	chr1:150533483-150536843	GM19099	blood:	n/a	n/a
46	PBX3	chr1:150536027-150536609	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr1:150535754-150536912	SK-N-SH	brain:	n/a	n/a
48	WRNIP1	chr1:150534615-150536633	GM12878	blood:	n/a	n/a
49	RUNX3	chr1:150533391-150536726	GM12878	blood:	n/a	chr1:150535341-150535350 chr1:150535341-150535350
50	POLR2A	chr1:150533481-150536822	Raji	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150488041..150489716-chr1:150536057..150538087,2	MCF-7	breast:
2	chr1:150458661..150461236-chr1:150531725..150536785,4	MCF-7	breast:
3	chr1:150449166..150451337-chr1:150534511..150537297,2	MCF-7	breast:
4	chr1:150336838..150338667-chr1:150536131..150537830,2	MCF-7	breast:
5	chr1:150531290..150540028-chr1:150591374..150603951,29	MCF-7	breast:
6	chr1:150534907..150536972-chr1:150946093..150948394,2	K562	blood:
7	chr1:150536175..150539015-chr1:151037065..151039505,2	K562	blood:
8	chr1:150532182..150537720-chr1:150588719..150604935,28	MCF-7	breast:
9	chr1:150443594..150446191-chr1:150534079..150536704,3	K562	blood:
10	chr1:150534473..150536412-chr1:150947180..150948692,2	MCF-7	breast:
11	chr1:150206817..150208988-chr1:150534242..150536753,3	MCF-7	breast:
12	chr1:150460339..150462002-chr1:150534789..150536958,2	K562	blood:

Variant related genes	Relation type
ADAMTSL4-AS1	TF binding region
ENSG00000228126	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000143374	Chromatin interaction
ENSG00000143420	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000143401	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1053701	0.91[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[MKK][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11204674	0.91[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes]
rs11205367	1.00[AFR][1000 genomes]
rs11205374	1.00[AFR][1000 genomes]
rs11205377	1.00[AFR][1000 genomes]
rs11576175	0.91[CEU][hapmap];0.81[JPT][hapmap];1.00[MKK][hapmap]
rs11576289	1.00[AFR][1000 genomes]
rs11576293	1.00[AFR][1000 genomes]
rs11577751	1.00[AFR][1000 genomes]
rs11578585	1.00[AFR][1000 genomes]
rs11579341	1.00[AFR][1000 genomes]
rs11580764	1.00[AFR][1000 genomes]
rs11585460	0.82[ASN][1000 genomes]
rs11586880	1.00[AFR][1000 genomes]
rs11587682	1.00[AFR][1000 genomes]
rs11587837	1.00[AFR][1000 genomes]
rs11588221	1.00[AFR][1000 genomes]
rs12034302	0.91[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12036914	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12038403	0.91[CEU][hapmap];0.81[JPT][hapmap]
rs12042580	0.83[ASN][1000 genomes]
rs12045807	0.84[CEU][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs12119320	1.00[AFR][1000 genomes]
rs12120428	1.00[AFR][1000 genomes]
rs12120867	1.00[AFR][1000 genomes]
rs12126312	1.00[AFR][1000 genomes]
rs12128385	1.00[AFR][1000 genomes]
rs12132918	1.00[AFR][1000 genomes]
rs12138453	1.00[AFR][1000 genomes]
rs12142331	1.00[AFR][1000 genomes]
rs12142874	1.00[AFR][1000 genomes]
rs12144958	1.00[AFR][1000 genomes]
rs16840074	0.91[CEU][hapmap]
rs2133128	1.00[AFR][1000 genomes]
rs28744536	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34848955	1.00[AFR][1000 genomes]
rs3754207	0.91[CEU][hapmap];0.81[JPT][hapmap];1.00[MKK][hapmap]
rs41264469	1.00[AFR][1000 genomes]
rs41273537	1.00[AFR][1000 genomes]
rs41300865	1.00[AFR][1000 genomes]
rs4265470	1.00[AFR][1000 genomes]
rs55973252	1.00[AFR][1000 genomes]
rs60060012	0.86[ASN][1000 genomes]
rs61820166	0.86[ASN][1000 genomes]
rs61820168	0.85[ASN][1000 genomes]
rs61820170	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6587515	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6672667	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72696841	1.00[AFR][1000 genomes]
rs72696852	1.00[AFR][1000 genomes]
rs72696855	1.00[AFR][1000 genomes]
rs72696873	1.00[AFR][1000 genomes]
rs72696880	1.00[AFR][1000 genomes]
rs72698822	1.00[AFR][1000 genomes]
rs72698842	1.00[AFR][1000 genomes]
rs72698892	1.00[AFR][1000 genomes]
rs72700804	1.00[AFR][1000 genomes]
rs72700810	1.00[AFR][1000 genomes]
rs72700813	1.00[AFR][1000 genomes]
rs7517	0.84[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs7543465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][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	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
2	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
3	esv1814231	chr1:150479528-150540117	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	71 gene(s)	inside rSNPs	diseases
4	nsv527379	chr1:150527354-150542128	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
5	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11204665	CTSK	cis	lymphoblastoid	seeQTL
rs11204665	PLEKHO1	cis	lymphoblastoid	seeQTL
rs11204665	ARNT	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150529800-150536800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:150532400-150537000	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr1:150532400-150537000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr1:150532600-150536400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:150532600-150536800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr1:150532600-150536800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:150532800-150536600	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr1:150533200-150536400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr1:150533400-150536600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:150533400-150536600	Flanking Active TSS	Fetal Thymus	thymus
11	chr1:150533400-150536800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr1:150533600-150536800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:150533600-150537400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:150534000-150536600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr1:150534000-150536800	Flanking Active TSS	Primary B cells from peripheral blood	blood
16	chr1:150534000-150536800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr1:150534200-150536400	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr1:150534200-150536600	Flanking Active TSS	Colonic Mucosa	Colon
19	chr1:150534200-150536600	Flanking Active TSS	A549	lung
20	chr1:150534200-150536800	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr1:150534200-150536800	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr1:150534200-150536800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr1:150534200-150536800	Flanking Active TSS	Hela-S3	cervix
24	chr1:150534200-150537000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr1:150534200-150537000	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr1:150534400-150539200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:150534400-150547200	Weak transcription	Ovary	ovary
28	chr1:150534600-150536600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:150534600-150537000	Enhancers	Fetal Kidney	kidney
30	chr1:150534600-150537600	Enhancers	Placenta Amnion	Placenta Amnion
31	chr1:150534600-150537600	Enhancers	NHLF	lung
32	chr1:150534600-150539200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:150534600-150540200	Enhancers	Pancreas	Pancrea
34	chr1:150534600-150542600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:150534600-150542600	Enhancers	Lung	lung
36	chr1:150534800-150536600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:150534800-150536800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr1:150534800-150536800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:150534800-150536800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr1:150534800-150536800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr1:150534800-150537000	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr1:150534800-150537200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr1:150534800-150538400	Flanking Active TSS	GM12878-XiMat	blood
44	chr1:150534800-150539800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:150534800-150540400	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr1:150535000-150536800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr1:150535000-150536800	Enhancers	Brain Cingulate Gyrus	brain
48	chr1:150535000-150536800	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr1:150535000-150536800	Flanking Active TSS	HepG2	liver
50	chr1:150535000-150537200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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