Variant report

Variant	rs6678384
Chromosome Location	chr1:181011529-181011530
allele	G/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180990073..180993369-chr1:181008815..181014232,9	MCF-7	breast:
2	chr1:181004788..181008643-chr1:181010792..181015908,7	K562	blood:
3	chr1:181010770..181016050-chr1:181055138..181060794,9	MCF-7	breast:
4	chr1:181001684..181003948-chr1:181009601..181013491,4	K562	blood:
5	chr1:181009038..181012023-chr1:181029706..181032224,2	K562	blood:
6	chr1:181011084..181016329-chr1:181056547..181060434,6	K562	blood:
7	chr1:180999745..181016101-chr1:181055432..181063450,33	K562	blood:
8	chr1:181004593..181007804-chr1:181008315..181013552,8	K562	blood:
9	chr1:181003253..181008679-chr1:181011469..181014538,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162783	Chromatin interaction
ENSG00000153029	Chromatin interaction
ENSG00000272198	Chromatin interaction
ENSG00000135823	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11589765	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12073184	0.90[ASN][1000 genomes]
rs12727543	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61809217	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6425661	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6692913	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	esv3342865	chr1:180933678-181018012	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3383831	chr1:180937224-181029755	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1011081	chr1:180973159-181135953	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:181002600-181012200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:181003800-181012200	Weak transcription	Placenta	Placenta
3	chr1:181004000-181012000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:181004000-181012000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:181004000-181013600	Weak transcription	Psoas Muscle	Psoas
6	chr1:181004000-181015600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:181004000-181025400	Weak transcription	Fetal Stomach	stomach
8	chr1:181004000-181025800	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:181004000-181026200	Weak transcription	Brain Anterior Caudate	brain
10	chr1:181004200-181012200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:181005000-181011800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:181005200-181011800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:181005200-181012200	Weak transcription	Lung	lung
14	chr1:181005400-181012000	Weak transcription	Adipose Nuclei	Adipose
15	chr1:181005400-181012200	Weak transcription	Colonic Mucosa	Colon
16	chr1:181005600-181012200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:181005600-181013800	Weak transcription	Pancreas	Pancrea
18	chr1:181005600-181025800	Weak transcription	Right Ventricle	heart
19	chr1:181005600-181026000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:181005600-181026400	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:181005600-181028200	Weak transcription	Gastric	stomach
22	chr1:181005600-181028600	Weak transcription	Ovary	ovary
23	chr1:181005800-181012000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:181005800-181012200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:181005800-181012200	Weak transcription	Esophagus	oesophagus
26	chr1:181005800-181012200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:181006000-181012200	Weak transcription	Thymus	Thymus
28	chr1:181006200-181012200	Weak transcription	Small Intestine	intestine
29	chr1:181006400-181012000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:181006400-181012000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:181006800-181012000	Weak transcription	Primary B cells from cord blood	blood
32	chr1:181006800-181012000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:181006800-181012200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:181007200-181012000	Weak transcription	Primary T cells from cord blood	blood
35	chr1:181007200-181026600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:181008000-181012000	Weak transcription	K562	blood
37	chr1:181008600-181011800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:181008600-181011800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:181008600-181011800	Weak transcription	Hela-S3	cervix
40	chr1:181008600-181012000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:181008600-181012000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:181008600-181012000	Weak transcription	Dnd41	blood
43	chr1:181008600-181012200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:181008600-181020800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:181008600-181031400	Weak transcription	NHLF	lung
46	chr1:181008800-181012200	Weak transcription	Fetal Thymus	thymus
47	chr1:181008800-181022800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:181009600-181014600	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr1:181009800-181011800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:181009800-181011800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links