Variant report

Variant	rs379508
Chromosome Location	chr6:5112912-5112913
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	chr6:5112432-5113244	SK-N-SH	brain:	n/a	n/a
2	NR3C1	chr6:5112677-5113080	A549	lung:	n/a	chr6:5112703-5112729 chr6:5112703-5112729
3	NR3C1	chr6:5112642-5112992	A549	lung:	n/a	chr6:5112703-5112729 chr6:5112703-5112729
4	TEAD4	chr6:5112598-5113224	SK-N-SH	brain:	n/a	n/a
5	MAX	chr6:5112648-5113195	SK-N-SH	brain:	n/a	n/a
6	EP300	chr6:5112692-5113062	SK-N-SH_RA	brain:	n/a	n/a
7	NR3C1	chr6:5112685-5112966	A549	lung:	n/a	chr6:5112703-5112729 chr6:5112703-5112729
8	MYC	chr6:5112756-5112966	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr6:5112868-5112992	MCF10A-Er-Src	breast:	n/a	n/a
10	PBX3	chr6:5112520-5113217	SK-N-SH	brain:	n/a	n/a
11	MAX	chr6:5112695-5113145	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr6:5112595-5113222	SK-N-SH	brain:	n/a	n/a
13	PBX3	chr6:5112483-5113328	SK-N-SH	brain:	n/a	n/a
14	FOSL2	chr6:5112670-5113153	A549	lung:	n/a	n/a
15	RCOR1	chr6:5112592-5113315	IMR90	lung:	n/a	n/a
16	EP300	chr6:5112470-5113301	SK-N-SH	brain:	n/a	n/a
17	FOS	chr6:5112766-5112913	MCF10A-Er-Src	breast:	n/a	n/a
18	MYC	chr6:5112695-5113043	MCF10A-Er-Src	breast:	n/a	n/a
19	NFIC	chr6:5112532-5113140	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr6:5112662-5113088	SK-N-SH	brain:	n/a	n/a
21	FOSL2	chr6:5112518-5113274	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr6:5112808-5112968	Hela-S3	cervix:	n/a	n/a
23	JUND	chr6:5112578-5113207	SK-N-SH	brain:	n/a	n/a
24	MAX	chr6:5112627-5113209	A549	lung:	n/a	n/a
25	EP300	chr6:5112666-5113074	SK-N-SH_RA	brain:	n/a	n/a
26	GATA3	chr6:5112539-5113318	SK-N-SH	brain:	n/a	n/a
27	REST	chr6:5112805-5113099	SK-N-SH	brain:	n/a	n/a
28	FOS	chr6:5112755-5113055	MCF10A-Er-Src	breast:	n/a	n/a
29	JUND	chr6:5112385-5113258	SK-N-SH	brain:	n/a	n/a
30	TCF12	chr6:5112470-5113290	SK-N-SH	brain:	n/a	n/a
31	NR3C1	chr6:5112542-5113092	A549	lung:	n/a	chr6:5112703-5112729 chr6:5112703-5112729

Variant related genes	Relation type
LYRM4	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs200844	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs200860	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs200866	0.90[AMR][1000 genomes]
rs200869	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs364857	0.85[ASN][1000 genomes]
rs373696	0.93[ASN][1000 genomes]
rs374117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs379511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs392847	0.95[ASN][1000 genomes]
rs393055	0.85[ASN][1000 genomes]
rs393300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs393628	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs394252	0.87[ASN][1000 genomes]
rs411483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411893	0.83[ASN][1000 genomes]
rs414986	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs417629	0.95[ASN][1000 genomes]
rs424006	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs434706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438934	0.93[ASN][1000 genomes]
rs439911	0.93[ASN][1000 genomes]
rs441463	0.85[ASN][1000 genomes]
rs441482	0.85[ASN][1000 genomes]
rs445229	0.83[ASN][1000 genomes]
rs445342	0.93[ASN][1000 genomes]
rs452908	0.85[ASN][1000 genomes]
rs453331	0.93[ASN][1000 genomes]
rs458108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs458283	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs458743	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs461117	0.81[EUR][1000 genomes]
rs461465	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs462327	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs465453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs465481	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs466285	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs591481	0.85[ASN][1000 genomes]
rs592775	0.81[EUR][1000 genomes]
rs606033	0.86[ASN][1000 genomes]
rs620360	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs661578	0.85[ASN][1000 genomes]
rs667543	0.93[ASN][1000 genomes]
rs9405257	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1017373	chr6:5066785-5128943	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv538112	chr6:5066785-5128943	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	esv12148	chr6:5112412-5112918	Genic enhancers Weak transcription Enhancers Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5095800-5114200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:5098600-5117000	Weak transcription	Fetal Brain Female	brain
3	chr6:5099000-5130000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:5101800-5132200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:5103000-5113000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:5103200-5113600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:5103200-5114000	Weak transcription	Dnd41	blood
8	chr6:5103200-5132800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:5105000-5113200	Strong transcription	HepG2	liver
10	chr6:5105200-5115800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:5105200-5131400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:5105800-5125600	Weak transcription	Ovary	ovary
13	chr6:5105800-5128200	Weak transcription	Primary B cells from cord blood	blood
14	chr6:5107800-5132000	Weak transcription	Pancreas	Pancrea
15	chr6:5108000-5113600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:5109000-5113800	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:5109000-5116400	Weak transcription	Brain Germinal Matrix	brain
18	chr6:5109200-5118600	Weak transcription	Esophagus	oesophagus
19	chr6:5109200-5121800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:5109200-5130200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:5109400-5121600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr6:5109800-5113800	Weak transcription	Colonic Mucosa	Colon
23	chr6:5110000-5114000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr6:5110200-5113000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:5110200-5121800	Weak transcription	Brain Anterior Caudate	brain
26	chr6:5110400-5121600	Weak transcription	Adipose Nuclei	Adipose
27	chr6:5110600-5113800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:5111200-5119200	Weak transcription	Fetal Intestine Large	intestine
29	chr6:5111600-5113000	Strong transcription	Gastric	stomach
30	chr6:5111600-5113200	Enhancers	Fetal Heart	heart
31	chr6:5111600-5113200	Enhancers	Left Ventricle	heart
32	chr6:5111600-5113600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:5111600-5113600	Strong transcription	Fetal Intestine Small	intestine
34	chr6:5111800-5113000	Genic enhancers	Fetal Muscle Leg	muscle
35	chr6:5111800-5113000	Enhancers	Fetal Thymus	thymus
36	chr6:5111800-5113200	Genic enhancers	Fetal Stomach	stomach
37	chr6:5111800-5113400	Strong transcription	Stomach Smooth Muscle	stomach
38	chr6:5111800-5113800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:5112000-5113400	Enhancers	NHDF-Ad	bronchial
40	chr6:5112000-5113600	Enhancers	HMEC	breast
41	chr6:5112000-5114000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr6:5112200-5113200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:5112200-5113200	Enhancers	Muscle Satellite Cultured Cells	--
44	chr6:5112200-5113400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:5112200-5113400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:5112200-5113600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:5112200-5113600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:5112200-5128600	Weak transcription	Primary T cells from cord blood	blood
49	chr6:5112400-5113000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:5112400-5113200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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