Variant report

Variant	rs52401
Chromosome Location	chr6:5146147-5146148
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5145534..5146304-chr8:93741632..93742260,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs175596	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200859	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200860	0.92[ASN][1000 genomes]
rs200862	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200866	0.92[ASN][1000 genomes]
rs200867	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200868	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200869	0.92[ASN][1000 genomes]
rs200870	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143693	0.82[ASN][1000 genomes]
rs2746235	0.84[AMR][1000 genomes]
rs2746239	0.82[ASN][1000 genomes]
rs393055	0.80[ASN][1000 genomes]
rs399120	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414986	0.88[ASN][1000 genomes]
rs450176	0.82[ASN][1000 genomes]
rs458283	0.80[ASN][1000 genomes]
rs458743	0.80[ASN][1000 genomes]
rs460416	0.88[ASN][1000 genomes]
rs461465	0.80[ASN][1000 genomes]
rs462327	0.80[ASN][1000 genomes]
rs462487	0.96[ASN][1000 genomes]
rs465481	0.80[ASN][1000 genomes]
rs466285	0.80[ASN][1000 genomes]
rs7752848	0.82[ASN][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

No data

Chromatin state (count:32 , 50 per page) page: 1

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	chr6:5133400-5151600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:5133800-5153400	Weak transcription	Right Ventricle	heart
5	chr6:5135000-5151000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:5135200-5151800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:5136400-5151000	Weak transcription	NHEK	skin
8	chr6:5136400-5151600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:5137000-5166600	Weak transcription	Primary T cells from cord blood	blood
10	chr6:5140000-5148600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:5141000-5149200	Weak transcription	Primary B cells from cord blood	blood
12	chr6:5143400-5146200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:5143600-5152400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:5143600-5172400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:5144000-5152400	Weak transcription	Spleen	Spleen
16	chr6:5144000-5152800	Weak transcription	Left Ventricle	heart
17	chr6:5144000-5175400	Weak transcription	HepG2	liver
18	chr6:5144400-5146400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:5144400-5147000	Weak transcription	Fetal Kidney	kidney
20	chr6:5144400-5151800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:5144400-5152800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:5144400-5157200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:5144600-5146200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr6:5144600-5152400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:5145000-5146400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr6:5145000-5147000	Enhancers	Fetal Muscle Trunk	muscle
27	chr6:5145000-5147000	Enhancers	Fetal Muscle Leg	muscle
28	chr6:5145400-5180800	Weak transcription	Fetal Intestine Small	intestine
29	chr6:5145600-5156600	Weak transcription	Fetal Stomach	stomach
30	chr6:5146000-5146200	Enhancers	Psoas Muscle	Psoas
31	chr6:5146000-5147400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:5146000-5147400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links