Variant report

Variant	rs56123606
Chromosome Location	chr6:30811625-30811626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30709488..30712315-chr6:30811079..30813946,2	MCF-7	breast:
2	chr6:30811247..30813730-chr6:30844224..30845960,2	K562	blood:
3	chr6:30710179..30712517-chr6:30808321..30811657,4	MCF-7	breast:
4	chr6:30708712..30711147-chr6:30810186..30812455,3	K562	blood:
5	chr6:30810334..30813136-chr6:30813626..30816587,2	K562	blood:
6	chr6:30796462..30798109-chr6:30809712..30812488,2	K562	blood:
7	chr6:30809749..30812115-chr6:30849210..30852847,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SFTA2-12	chr6:30811155-30812133	NONHSAT108684

No data

Variant related genes	Relation type
ENSG00000272273	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000237923	Chromatin interaction
ENSG00000204580	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1264361	1.00[ASN][1000 genomes]
rs3095334	1.00[ASN][1000 genomes]
rs3129978	1.00[ASN][1000 genomes]
rs3129980	1.00[ASN][1000 genomes]
rs3129981	1.00[ASN][1000 genomes]
rs3129982	1.00[ASN][1000 genomes]
rs3129983	1.00[ASN][1000 genomes]
rs3129985	1.00[ASN][1000 genomes]
rs3130641	1.00[ASN][1000 genomes]
rs3130665	1.00[ASN][1000 genomes]
rs3130669	1.00[ASN][1000 genomes]
rs3130673	1.00[ASN][1000 genomes]
rs3131041	1.00[ASN][1000 genomes]
rs3131044	1.00[ASN][1000 genomes]
rs3131045	1.00[ASN][1000 genomes]
rs3131047	1.00[ASN][1000 genomes]
rs3131048	1.00[ASN][1000 genomes]
rs3131049	1.00[ASN][1000 genomes]
rs3131050	1.00[ASN][1000 genomes]
rs3131055	1.00[ASN][1000 genomes]
rs3131058	1.00[ASN][1000 genomes]
rs3131060	1.00[ASN][1000 genomes]
rs3132599	1.00[ASN][1000 genomes]
rs3132605	1.00[ASN][1000 genomes]
rs45565239	1.00[ASN][1000 genomes]
rs55694686	1.00[ASN][1000 genomes]
rs55702639	1.00[ASN][1000 genomes]
rs55707154	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55787895	1.00[AMR][1000 genomes]
rs55848160	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56051116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56105977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56111713	1.00[ASN][1000 genomes]
rs56133130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56183784	1.00[ASN][1000 genomes]
rs56327229	1.00[ASN][1000 genomes]
rs56377503	1.00[ASN][1000 genomes]
rs56804692	1.00[ASN][1000 genomes]
rs886424	1.00[ASN][1000 genomes]
rs886425	1.00[ASN][1000 genomes]
rs9262200	1.00[ASN][1000 genomes]
rs9262202	1.00[ASN][1000 genomes]
rs9262203	1.00[ASN][1000 genomes]
rs9262204	1.00[ASN][1000 genomes]
rs9468857	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS 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	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS 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	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
8	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30797200-30812000	Weak transcription	Lung	lung
2	chr6:30799200-30812200	Weak transcription	Spleen	Spleen
3	chr6:30806800-30816200	Enhancers	Placenta	Placenta
4	chr6:30807400-30812200	Enhancers	Duodenum Mucosa	Duodenum
5	chr6:30808200-30812000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:30808200-30813600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:30809000-30811800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:30809600-30811800	Weak transcription	Esophagus	oesophagus
9	chr6:30810000-30813400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr6:30810600-30811800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr6:30810800-30811800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:30810800-30812000	Enhancers	Osteobl	bone
13	chr6:30810800-30812400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:30810800-30812600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:30810800-30812600	Enhancers	Fetal Lung	lung
16	chr6:30810800-30812800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr6:30810800-30813400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:30810800-30814000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
19	chr6:30811000-30811800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr6:30811000-30811800	Enhancers	Fetal Stomach	stomach
21	chr6:30811000-30811800	Enhancers	Small Intestine	intestine
22	chr6:30811000-30812000	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr6:30811000-30812200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:30811000-30812200	Enhancers	Aorta	Aorta
25	chr6:30811000-30812200	Enhancers	Fetal Intestine Large	intestine
26	chr6:30811000-30812200	Enhancers	Right Ventricle	heart
27	chr6:30811000-30812400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr6:30811000-30812400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr6:30811000-30812400	Enhancers	Fetal Muscle Trunk	muscle
30	chr6:30811000-30812400	Enhancers	Fetal Muscle Leg	muscle
31	chr6:30811000-30812600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:30811000-30812600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:30811000-30812600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:30811000-30812600	Enhancers	Gastric	stomach
35	chr6:30811000-30812600	Enhancers	Left Ventricle	heart
36	chr6:30811000-30812600	Enhancers	Right Atrium	heart
37	chr6:30811000-30812600	Enhancers	HSMM	muscle
38	chr6:30811000-30813200	Enhancers	Ovary	ovary
39	chr6:30811000-30813600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:30811000-30813600	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr6:30811000-30813800	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr6:30811000-30814000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:30811000-30814200	Genic enhancers	H1 Cell Line	embryonic stem cell
44	chr6:30811200-30811800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:30811200-30811800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:30811200-30811800	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr6:30811200-30812000	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr6:30811200-30812000	Enhancers	Fetal Kidney	kidney
49	chr6:30811200-30812000	Weak transcription	Pancreas	Pancrea
50	chr6:30811200-30812000	Enhancers	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links