Variant report

Variant	rs450176
Chromosome Location	chr6:5152456-5152457
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	TCF12	chr6:5151609-5152853	SK-N-SH	brain:	n/a	n/a
2	STAT3	chr6:5152144-5152467	MCF10A-Er-Src	breast:	n/a	n/a
3	EP300	chr6:5151904-5152665	SK-N-SH	brain:	n/a	chr6:5152615-5152622
4	JUND	chr6:5151916-5152737	SK-N-SH	brain:	n/a	n/a
5	CEBPB	chr6:5152046-5152557	IMR90	lung:	n/a	n/a
6	FOS	chr6:5152083-5152467	MCF10A-Er-Src	breast:	n/a	n/a
7	RAD21	chr6:5152109-5152514	IMR90	lung:	n/a	n/a
8	POLR2A	chr6:5152077-5152472	SK-N-SH	brain:	n/a	n/a
9	MAX	chr6:5152071-5152790	SK-N-SH	brain:	n/a	n/a
10	FOSL2	chr6:5152052-5152604	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr6:5151496-5152753	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr6:5151595-5152666	SK-N-SH	brain:	n/a	n/a
13	STAT3	chr6:5152143-5152504	MCF10A-Er-Src	breast:	n/a	n/a
14	YY1	chr6:5151965-5152570	SK-N-SH	brain:	n/a	n/a
15	FOSL2	chr6:5151899-5152775	SK-N-SH	brain:	n/a	n/a
16	PBX3	chr6:5151772-5152821	SK-N-SH	brain:	n/a	n/a
17	TAF1	chr6:5152407-5152581	SK-N-SH	brain:	n/a	n/a
18	PBX3	chr6:5151936-5152757	SK-N-SH	brain:	n/a	n/a
19	NFIC	chr6:5151869-5152823	SK-N-SH	brain:	n/a	n/a
20	GATA2	chr6:5151562-5152536	SH-SY5Y	brain:	n/a	n/a
21	TCF12	chr6:5151856-5152755	SK-N-SH	brain:	n/a	n/a
22	JUND	chr6:5151727-5152766	SK-N-SH	brain:	n/a	n/a
23	STAT3	chr6:5152160-5152486	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
MIR3691	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1571564	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs175596	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1888147	0.87[AMR][1000 genomes]
rs200859	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs200862	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs200866	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs200867	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs200868	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs200870	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2143693	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs2746235	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2746239	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399120	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs424006	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs458743	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs460416	1.00[JPT][hapmap]
rs460440	0.85[MEX][hapmap]
rs462327	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs462487	1.00[JPT][hapmap]
rs465481	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs466285	0.88[JPT][hapmap]
rs4960069	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs52401	0.82[ASN][1000 genomes]
rs6597117	0.87[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7752848	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7766717	0.87[CEU][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
8	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1017821	chr6:5114609-5213200	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
12	nsv538114	chr6:5114609-5213200	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
13	nsv5179	chr6:5121824-5167027	Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
15	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
16	nsv1022336	chr6:5145194-5200687	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
17	nsv1018984	chr6:5145194-5200801	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs450176	LYRM4	cis	parietal	SCAN
rs450176	LYRM4	cis	cerebellum	SCAN
rs450176	TUBB2B	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5129000-5162000	Weak transcription	K562	blood
2	chr6:5130600-5172200	Weak transcription	Lung	lung
3	chr6:5133800-5153400	Weak transcription	Right Ventricle	heart
4	chr6:5137000-5166600	Weak transcription	Primary T cells from cord blood	blood
5	chr6:5143600-5172400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:5144000-5152800	Weak transcription	Left Ventricle	heart
7	chr6:5144000-5175400	Weak transcription	HepG2	liver
8	chr6:5144400-5152800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:5144400-5157200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:5145400-5180800	Weak transcription	Fetal Intestine Small	intestine
11	chr6:5145600-5156600	Weak transcription	Fetal Stomach	stomach
12	chr6:5147400-5158000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:5150800-5153000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:5150800-5153000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:5151000-5153200	Enhancers	HMEC	breast
16	chr6:5151000-5153200	Enhancers	Osteobl	bone
17	chr6:5151600-5152600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:5151600-5152800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:5151600-5152800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:5151600-5152800	Flanking Active TSS	NHEK	skin
21	chr6:5151600-5153000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:5151600-5153000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:5151600-5153000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr6:5151600-5153000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:5151600-5153000	Enhancers	NHLF	lung
26	chr6:5151600-5153200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:5151600-5153600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr6:5151800-5153000	Enhancers	Stomach Smooth Muscle	stomach
29	chr6:5151800-5153200	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr6:5151800-5153200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:5152000-5152800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:5152000-5152800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:5152200-5152600	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr6:5152200-5152800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr6:5152200-5153000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:5152200-5153000	Flanking Active TSS	HSMM	muscle
37	chr6:5152200-5153000	Flanking Active TSS	HSMMtube	muscle
38	chr6:5152200-5153000	Flanking Active TSS	NH-A	brain
39	chr6:5152400-5152600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:5152400-5152600	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr6:5152400-5152600	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr6:5152400-5152600	Flanking Active TSS	Brain Substantia Nigra	brain
43	chr6:5152400-5152600	Enhancers	Fetal Brain Female	brain
44	chr6:5152400-5152600	Enhancers	Spleen	Spleen
45	chr6:5152400-5152800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:5152400-5152800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:5152400-5152800	Flanking Active TSS	Brain Angular Gyrus	brain
48	chr6:5152400-5153000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr6:5152400-5153000	Enhancers	Adipose Nuclei	Adipose
50	chr6:5152400-5153000	Flanking Active TSS	NHDF-Ad	bronchial

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