Variant report

Variant	rs73365168
Chromosome Location	chr6:5032640-5032641
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:5032382..5034589-chr6:5044699..5046553,2	MCF-7	breast:
2	chr6:3924356..3927289-chr6:5032549..5034643,2	MCF-7	breast:
3	chr6:5002773..5004480-chr6:5029318..5032794,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPP40-1	chr6:5031990-5034916	ENSG00000248284

Variant related genes	Relation type
ENSG00000252419	Chromatin interaction
ENSG00000124787	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12332997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34008599	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55796617	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56193336	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56346886	1.00[EUR][1000 genomes]
rs57093437	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58769332	0.83[EUR][1000 genomes]
rs59365793	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73349204	1.00[AMR][1000 genomes]
rs73353056	0.86[EUR][1000 genomes]
rs73353059	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73353070	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73359952	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73365181	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9504306	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers 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 target site	13 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5027000-5032800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:5027000-5032800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr6:5027000-5033000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:5027000-5033000	Weak transcription	Colonic Mucosa	Colon
5	chr6:5027000-5033200	Weak transcription	Esophagus	oesophagus
6	chr6:5027000-5036400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:5027200-5032800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:5027200-5032800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:5027200-5032800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:5027200-5032800	Weak transcription	HMEC	breast
11	chr6:5027200-5033000	Weak transcription	Fetal Intestine Small	intestine
12	chr6:5027200-5033000	Weak transcription	Right Atrium	heart
13	chr6:5027200-5034600	Weak transcription	Fetal Thymus	thymus
14	chr6:5027200-5047200	Weak transcription	Adipose Nuclei	Adipose
15	chr6:5027400-5032800	Weak transcription	Fetal Stomach	stomach
16	chr6:5027400-5033200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:5029400-5034200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:5029800-5033000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:5030600-5034200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:5030800-5032800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:5031000-5034400	Weak transcription	Osteobl	bone
22	chr6:5031200-5033200	Weak transcription	Right Ventricle	heart
23	chr6:5031200-5034000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:5031200-5034200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:5031200-5042800	Weak transcription	Ovary	ovary
26	chr6:5031400-5036400	Weak transcription	K562	blood
27	chr6:5031600-5032800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:5031600-5033000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:5031600-5033000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:5031600-5033000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:5031600-5033000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:5031600-5033000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:5031600-5034000	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:5031600-5034200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr6:5031600-5034200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr6:5031600-5042800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr6:5031800-5033000	Weak transcription	Placenta	Placenta
38	chr6:5031800-5034200	Weak transcription	Thymus	Thymus
39	chr6:5031800-5043800	Weak transcription	Spleen	Spleen
40	chr6:5032000-5033000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr6:5032000-5033000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr6:5032600-5032800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr6:5032600-5032800	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr6:5032600-5032800	Flanking Active TSS	A549	lung
45	chr6:5032600-5032800	Enhancers	Hela-S3	cervix
46	chr6:5032600-5032800	Enhancers	NHDF-Ad	bronchial
47	chr6:5032600-5032800	Enhancers	NHEK	skin
48	chr6:5032600-5033000	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr6:5032600-5033000	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr6:5032600-5033000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links