Variant report

Variant	rs6544977
Chromosome Location	chr2:47538696-47538697
allele	C/T
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47398263..47400819-chr2:47535902..47539310,3	MCF-7	breast:
2	chr2:47497085..47500611-chr2:47536768..47542000,5	MCF-7	breast:
3	chr2:47400906..47404753-chr2:47537729..47542393,7	K562	blood:
4	chr2:47484907..47487691-chr2:47537998..47540453,2	MCF-7	breast:
5	chr2:47527356..47529595-chr2:47537619..47539608,2	K562	blood:
6	chr2:47402318..47405024-chr2:47536306..47539127,3	MCF-7	breast:
7	chr2:47385656..47388232-chr2:47538182..47540860,2	MCF-7	breast:
8	chr2:47395267..47408439-chr2:47533772..47553038,55	MCF-7	breast:
9	chr2:47398506..47400133-chr2:47537850..47540802,2	K562	blood:
10	chr2:47400534..47404753-chr2:47537729..47541997,7	K562	blood:
11	chr2:47498345..47500843-chr2:47537583..47540511,2	MCF-7	breast:
12	chr2:47536098..47538713-chr2:47547950..47550505,2	MCF-7	breast:
13	chr2:47424415..47427832-chr2:47536667..47539203,3	MCF-7	breast:
14	chr2:47529427..47534518-chr2:47538025..47540772,4	MCF-7	breast:
15	chr2:47538622..47541292-chr2:47546118..47547816,2	MCF-7	breast:
16	chr2:47500714..47503481-chr2:47536098..47539031,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10180711	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10192326	0.88[CHB][hapmap]
rs12471906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4558636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4560164	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6544978	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6720211	0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9789479	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9789683	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS 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	50 gene(s)	inside rSNPs	diseases
4	nsv457385	chr2:47468331-47552277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv581755	chr2:47468331-47552277	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47520800-47540000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:47530400-47541200	Enhancers	Fetal Intestine Small	intestine
3	chr2:47530400-47541600	Enhancers	Fetal Intestine Large	intestine
4	chr2:47534400-47550400	Weak transcription	Ovary	ovary
5	chr2:47535000-47538800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:47535000-47540600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:47536200-47539400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:47536200-47540000	Enhancers	Primary B cells from peripheral blood	blood
9	chr2:47536200-47541400	Enhancers	Stomach Mucosa	stomach
10	chr2:47536400-47539000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:47536600-47538800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:47536600-47539000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr2:47536600-47539600	Enhancers	Placenta	Placenta
14	chr2:47536600-47541000	Enhancers	Primary hematopoietic stem cells	blood
15	chr2:47536800-47538800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:47536800-47538800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:47536800-47538800	Enhancers	Adipose Nuclei	Adipose
18	chr2:47536800-47538800	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr2:47536800-47538800	Enhancers	Fetal Heart	heart
20	chr2:47536800-47538800	Enhancers	Psoas Muscle	Psoas
21	chr2:47536800-47538800	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr2:47536800-47538800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:47536800-47538800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr2:47536800-47538800	Enhancers	Thymus	Thymus
25	chr2:47536800-47538800	Enhancers	Spleen	Spleen
26	chr2:47536800-47539000	Enhancers	Brain Germinal Matrix	brain
27	chr2:47536800-47539200	Enhancers	Right Atrium	heart
28	chr2:47537000-47538800	Enhancers	Colon Smooth Muscle	Colon
29	chr2:47537000-47538800	Enhancers	Left Ventricle	heart
30	chr2:47537200-47538800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:47537200-47538800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:47537200-47538800	Enhancers	Pancreas	Pancrea
33	chr2:47537200-47538800	Enhancers	Rectal Smooth Muscle	rectum
34	chr2:47537400-47538800	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr2:47537400-47538800	Enhancers	Gastric	stomach
36	chr2:47537400-47538800	Enhancers	Right Ventricle	heart
37	chr2:47537400-47540200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:47537400-47541000	Enhancers	Brain Angular Gyrus	brain
39	chr2:47537600-47541400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:47537800-47538800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:47537800-47538800	Enhancers	Lung	lung
42	chr2:47537800-47538800	Flanking Active TSS	GM12878-XiMat	blood
43	chr2:47537800-47539200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:47537800-47541400	Enhancers	Brain Substantia Nigra	brain
45	chr2:47538000-47538800	Enhancers	Primary B cells from cord blood	blood
46	chr2:47538000-47538800	Enhancers	Small Intestine	intestine
47	chr2:47538000-47540000	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr2:47538000-47540600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:47538200-47538800	Enhancers	Colonic Mucosa	Colon
50	chr2:47538200-47540200	Weak transcription	K562	blood

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