Variant report

Variant	rs1558257
Chromosome Location	chr11:67180025-67180026
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	POLR2A	chr11:67179928-67180333	GM12878	blood:	n/a	n/a
2	STAT3	chr11:67179930-67180110	MCF10A-Er-Src	breast:	n/a	chr11:67180018-67180029
3	POLR2A	chr11:67179164-67180324	GM12878	blood:	n/a	n/a
4	STAT3	chr11:67179922-67180126	MCF10A-Er-Src	breast:	n/a	chr11:67180112-67180120 chr11:67180018-67180029
5	HMGN3	chr11:67180003-67180197	K562	blood:	n/a	n/a
6	STAT3	chr11:67179864-67180197	MCF10A-Er-Src	breast:	n/a	chr11:67180112-67180120 chr11:67180018-67180029
7	POLR2A	chr11:67179883-67180314	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr11:67178520-67181031	K562	blood:	n/a	n/a
9	POLR2A	chr11:67179889-67180269	GM12878	blood:	n/a	n/a
10	STAT3	chr11:67179920-67180131	MCF10A-Er-Src	breast:	n/a	chr11:67180112-67180120 chr11:67180018-67180029
11	STAT3	chr11:67179885-67180085	MCF10A-Er-Src	breast:	n/a	chr11:67180018-67180029

No.	Distal block	Cell Line	Cell type
1	chr11:67123397..67125760-chr11:67179408..67181042,2	K562	blood:
2	chr11:67179246..67180965-chr11:67201278..67203605,2	K562	blood:
3	chr11:67177386..67180366-chr17:57935264..57937336,3	MCF-7	breast:
4	chr11:67175949..67181191-chr11:67230601..67234346,6	K562	blood:
5	chr11:67178949..67181040-chr11:67275352..67277898,2	K562	blood:

Variant related genes	Relation type
CARNS1	TF binding region
ENSG00000175482	Chromatin interaction
ENSG00000172663	Chromatin interaction
ENSG00000255949	Chromatin interaction
ENSG00000167797	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10896172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12288048	0.82[JPT][hapmap];0.86[MEX][hapmap]
rs12791853	0.82[JPT][hapmap]
rs12803635	0.82[CEU][hapmap]
rs12805811	1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs1419861	0.82[JPT][hapmap]
rs1790731	0.82[JPT][hapmap]
rs1790735	0.82[JPT][hapmap]
rs1790737	1.00[GIH][hapmap];0.86[MEX][hapmap]
rs1790738	1.00[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs1790739	0.82[JPT][hapmap]
rs1894112	0.82[JPT][hapmap]
rs1944096	1.00[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs2066496	0.83[CHB][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap]
rs2286620	0.83[CHB][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs2298815	0.86[MEX][hapmap]
rs2514256	0.82[TSI][hapmap]
rs2532605	1.00[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs34087937	1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs35121740	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35821109	1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs35899279	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3737460	0.82[JPT][hapmap];0.86[MEX][hapmap]
rs4930192	0.81[CHB][hapmap]
rs4930197	1.00[GIH][hapmap]
rs872110	0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv897796	chr11:67021518-67186000	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv897797	chr11:67023040-67293234	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
4	nsv1043037	chr11:67027193-67357425	Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	nsv897801	chr11:67033076-67432479	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv1047890	chr11:67058231-67184436	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv1048230	chr11:67058231-67252397	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
8	nsv897804	chr11:67090571-67224278	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
9	nsv1039205	chr11:67135246-67252397	Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
10	esv1818769	chr11:67138811-67300457	Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
11	esv1798859	chr11:67139954-67272983	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
12	nsv897805	chr11:67155210-67283891	ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
13	nsv897806	chr11:67155210-67294308	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
14	nsv897807	chr11:67155210-67414492	Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
15	nsv897808	chr11:67155210-67419855	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
16	nsv897809	chr11:67156875-67276235	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
17	nsv516453	chr11:67164495-67186000	Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
18	nsv555254	chr11:67164495-67288594	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
19	nsv534229	chr11:67164667-67411909	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
20	nsv897810	chr11:67166310-67196237	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
21	nsv897811	chr11:67166984-67218909	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
22	nsv897812	chr11:67174597-67198887	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
23	nsv897813	chr11:67175692-67283891	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
24	nsv521723	chr11:67175692-67311258	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
25	nsv555255	chr11:67177797-67191449	Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1558257	SSH3	cis	Whole Blood	GTEx
rs1558257	RPS6KB2	cis	Lymphoblastoid	GTEx
rs1558257	RPS6KB2	cis	multi-tissue	Pritchard
rs1558257	RPS6KB2	cis	lymphoblastoid	seeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67170000-67182800	Weak transcription	Right Atrium	heart
2	chr11:67173800-67181000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr11:67174000-67182200	Enhancers	Brain Hippocampus Middle	brain
4	chr11:67174200-67181200	Enhancers	Brain Cingulate Gyrus	brain
5	chr11:67174400-67181200	Enhancers	Brain Angular Gyrus	brain
6	chr11:67174400-67181400	Bivalent Enhancer	Fetal Muscle Leg	muscle
7	chr11:67175400-67181200	Enhancers	Brain Anterior Caudate	brain
8	chr11:67176400-67182400	Enhancers	Primary hematopoietic stem cells	blood
9	chr11:67177000-67181200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr11:67177400-67181000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr11:67177400-67181200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:67177600-67181000	Enhancers	GM12878-XiMat	blood
13	chr11:67177800-67182400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr11:67177800-67182600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr11:67177800-67182600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr11:67177800-67183400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr11:67178000-67182400	Enhancers	Primary B cells from peripheral blood	blood
18	chr11:67178000-67182400	Enhancers	Primary T cells fromperipheralblood	blood
19	chr11:67178000-67182400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr11:67178000-67182600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr11:67178200-67180800	Enhancers	Spleen	Spleen
22	chr11:67178200-67181400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr11:67178200-67181600	Enhancers	Thymus	Thymus
24	chr11:67178200-67182400	Weak transcription	Lung	lung
25	chr11:67178400-67181200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:67178400-67181200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr11:67178400-67181200	Enhancers	Dnd41	blood
28	chr11:67178400-67181200	Enhancers	K562	blood
29	chr11:67178400-67181400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr11:67178400-67182400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr11:67178400-67182400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr11:67178400-67182600	Enhancers	Primary B cells from cord blood	blood
33	chr11:67178400-67182600	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr11:67178400-67184200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr11:67178600-67180800	Enhancers	Brain Substantia Nigra	brain
36	chr11:67178600-67181000	Enhancers	Gastric	stomach
37	chr11:67178600-67182400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:67178600-67182600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr11:67178800-67182600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:67179000-67180600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:67179000-67182400	Enhancers	Fetal Thymus	thymus
42	chr11:67179400-67181000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr11:67179400-67181200	Bivalent Enhancer	HepG2	liver
44	chr11:67179400-67182400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr11:67179600-67180200	Enhancers	Esophagus	oesophagus
46	chr11:67179800-67180400	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr11:67179800-67180400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr11:67179800-67180600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:67179800-67181000	Bivalent Enhancer	Stomach Mucosa	stomach
50	chr11:67180000-67180200	Enhancers	HMEC	breast

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