Variant report

Variant	rs11753652
Chromosome Location	chr6:166756991-166756992
allele	C/T
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	RELA	chr6:166755144-166757094	GM10847	blood:	n/a	n/a
2	SPI1	chr6:166756519-166757019	GM12891	blood:	n/a	chr6:166756809-166756822 chr6:166756812-166756821 chr6:166756810-166756823
3	SPI1	chr6:166756333-166757296	GM12878	blood:	n/a	chr6:166756809-166756822 chr6:166756812-166756821 chr6:166756810-166756823
4	POLR2A	chr6:166754998-166757076	HL-60	blood:	n/a	n/a
5	POLR2A	chr6:166755473-166757367	K562	blood:	n/a	n/a
6	POLR2A	chr6:166755470-166757207	GM18526	blood:	n/a	n/a
7	NRF1	chr6:166755648-166757017	SK-N-SH	brain:	n/a	chr6:166756112-166756126 chr6:166756114-166756125 chr6:166756115-166756129 chr6:166756115-166756126
8	TEAD4	chr6:166755836-166757023	K562	blood:	n/a	n/a
9	POLR2A	chr6:166755072-166758044	K562	blood:	n/a	n/a
10	PML	chr6:166755716-166757050	K562	blood:	n/a	n/a
11	SIN3A	chr6:166756878-166757041	GM12878	blood:	n/a	n/a
12	MTA3	chr6:166754882-166757246	GM12878	blood:	n/a	n/a
13	MYC	chr6:166755478-166757002	K562	blood:	n/a	chr6:166755809-166755819
14	POLR2A	chr6:166755004-166757144	IMR90	lung:	n/a	n/a
15	POLR2A	chr6:166754659-166757069	GM12892	blood:	n/a	n/a
16	IRF1	chr6:166755882-166757307	K562	blood:	n/a	chr6:166756744-166756756 chr6:166756744-166756761 chr6:166757042-166757049 chr6:166756744-166756756
17	EP300	chr6:166755783-166757027	GM12878	blood:	n/a	chr6:166755853-166755869 chr6:166756097-166756106
18	POLR2A	chr6:166754776-166757119	GM12892	blood:	n/a	n/a
19	POLR2A	chr6:166755260-166757203	GM15510	blood:	n/a	n/a
20	MXI1	chr6:166754970-166757179	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:166754842-166757788	GM12891	blood:	n/a	n/a
22	SMC3	chr6:166755921-166757007	GM12878	blood:	n/a	n/a
23	RELA	chr6:166754957-166757148	GM18505	blood:	n/a	n/a
24	POLR2A	chr6:166755200-166757220	MCF10A-Er-Src	breast:	n/a	n/a
25	HEY1	chr6:166755737-166757235	HepG2	liver:	n/a	chr6:166755859-166755874
26	POLR2A	chr6:166755438-166757252	Raji	blood:	n/a	n/a
27	JUND	chr6:166755484-166757023	K562	blood:	n/a	chr6:166755689-166755698
28	POLR2A	chr6:166755939-166757209	HepG2	liver:	n/a	n/a
29	POLR2A	chr6:166755006-166757200	GM18505	blood:	n/a	n/a
30	PML	chr6:166754754-166757109	GM12878	blood:	n/a	n/a
31	MYBL2	chr6:166755615-166757034	HepG2	liver:	n/a	n/a
32	POLR2A	chr6:166755073-166757075	NB4	blood:	n/a	n/a
33	POLR2A	chr6:166755735-166757413	HepG2	liver:	n/a	n/a
34	IRF1	chr6:166755720-166757093	K562	blood:	n/a	chr6:166756744-166756756 chr6:166756744-166756761 chr6:166757042-166757049 chr6:166756744-166756756
35	TBL1XR1	chr6:166755005-166757118	GM12878	blood:	n/a	n/a
36	RCOR1	chr6:166755410-166757173	K562	blood:	n/a	n/a
37	STAT1	chr6:166756863-166757017	GM12878	blood:	n/a	chr6:166757001-166757009
38	POLR2A	chr6:166755092-166757119	PBDE	blood:	n/a	n/a
39	POLR2A	chr6:166755368-166757284	HepG2	liver:	n/a	n/a
40	POLR2A	chr6:166755637-166757042	GM12892	blood:	n/a	n/a
41	RCOR1	chr6:166755619-166757008	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:166755527-166756996	PFSK-1	brain:	n/a	n/a
43	POLR2A	chr6:166755645-166757057	GM12891	blood:	n/a	n/a
44	POLR2A	chr6:166755454-166757227	K562	blood:	n/a	n/a
45	POLR2A	chr6:166754964-166757187	GM12878	blood:	n/a	n/a
46	SPI1	chr6:166756585-166757064	HL-60	blood:	n/a	chr6:166756809-166756822 chr6:166756812-166756821 chr6:166756810-166756823
47	POLR2A	chr6:166746365-166757465	GM12878	blood:	n/a	n/a
48	RELA	chr6:166755035-166757068	GM12891	blood:	n/a	n/a
49	EBF1	chr6:166756506-166756998	GM12878	blood:	n/a	n/a
50	MYC	chr6:166755044-166757199	NB4	blood:	n/a	chr6:166755809-166755819

No.	Distal block	Cell Line	Cell type
1	chr6:166751804..166757558-chr6:166793969..166799153,5	K562	blood:
2	chr1:90460546..90461351-chr6:166756027..166757000,2	NB4	blood:
3	chr6:166755930..166757619-chr6:166781019..166784045,3	MCF-7	breast:
4	chr6:166754173..166757774-chr6:166795355..166798060,3	MCF-7	breast:
5	chr6:166753320..166757958-chr6:166794622..166799153,8	K562	blood:
6	chr6:166719852..166722547-chr6:166755922..166758056,2	K562	blood:
7	chr6:166756132..166758070-chr6:166759956..166762577,2	MCF-7	breast:

Variant related genes	Relation type
SFT2D1	TF binding region
ENSG00000162664	Chromatin interaction
ENSG00000176381	Chromatin interaction
ENSG00000261420	Chromatin interaction
ENSG00000060762	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10455809	0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10455976	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10455977	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10455978	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10946158	0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10946160	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10946161	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11551053	0.89[ASN][1000 genomes]
rs11752886	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11755305	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12198613	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12209616	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12214281	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12214812	0.95[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1599841	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2294333	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294334	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4144886	0.95[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4144887	0.95[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4144888	0.95[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4709111	0.82[CHB][hapmap]
rs4710042	0.82[CHB][hapmap]
rs59337176	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66461381	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68016351	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6932631	0.91[CEU][hapmap]
rs73030701	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73263155	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73788236	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7753161	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7767887	0.82[ASN][1000 genomes]
rs7771603	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9348121	0.82[CHB][hapmap]
rs941683	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11753652		cis	Lymphoblastoid	GTEx
rs11753652	SFT2D1	Cis_1M	lymphoblastoid	RTeQTL
rs11753652	LOC401284	cis	multi-tissue	Pritchard
rs11753652	LOC135043	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166754800-166757000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr6:166754800-166757000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:166754800-166757000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:166754800-166757000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:166754800-166757000	Active TSS	Colonic Mucosa	Colon
6	chr6:166754800-166757200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:166755000-166757000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr6:166755000-166757000	Active TSS	H1 Cell Line	embryonic stem cell
9	chr6:166755000-166757000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:166755000-166757000	Active TSS	Left Ventricle	heart
11	chr6:166755000-166757000	Active TSS	Psoas Muscle	Psoas
12	chr6:166755000-166757200	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr6:166755000-166757200	Active TSS	A549	lung
14	chr6:166755000-166757200	Active TSS	NHLF	lung
15	chr6:166755200-166757000	Active TSS	Right Ventricle	heart
16	chr6:166755400-166757000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr6:166755400-166757200	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr6:166755400-166757200	Active TSS	Small Intestine	intestine
19	chr6:166756200-166757000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr6:166756200-166757000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr6:166756200-166757200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:166756200-166757200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr6:166756200-166757400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:166756400-166757000	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr6:166756400-166757000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:166756400-166757000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr6:166756400-166757000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr6:166756400-166757000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:166756400-166757000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr6:166756400-166757000	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr6:166756400-166757000	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr6:166756400-166757000	Flanking Active TSS	Fetal Brain Male	brain
33	chr6:166756400-166757000	Active TSS	Right Atrium	heart
34	chr6:166756400-166757000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr6:166756400-166757000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr6:166756400-166757000	Flanking Active TSS	HUVEC	blood vessel
37	chr6:166756400-166757000	Flanking Active TSS	NH-A	brain
38	chr6:166756400-166757200	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr6:166756400-166757200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr6:166756400-166757200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr6:166756400-166757200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr6:166756400-166757200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:166756400-166757200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr6:166756400-166757200	Flanking Active TSS	Dnd41	blood
45	chr6:166756600-166757000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:166756600-166757000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr6:166756600-166757000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr6:166756600-166757000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:166756600-166757000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:166756600-166757000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links