Variant report

Variant	rs884427
Chromosome Location	chr2:9783635-9783636
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:9768781..9770412-chr2:9782843..9784568,2	K562	blood:
2	chr2:9780247..9783706-chr2:9899815..9903353,3	K562	blood:
3	chr2:9782754..9784911-chr2:9790958..9792910,2	K562	blood:
4	chr2:9730159..9735372-chr2:9781969..9785269,4	K562	blood:
5	chr2:9776669..9780406-chr2:9782873..9785983,5	MCF-7	breast:
6	chr2:9779400..9780949-chr2:9782818..9785036,2	K562	blood:
7	chr2:9782654..9789334-chr2:9794560..9799702,7	MCF-7	breast:
8	chr2:9781325..9786143-chr2:9786474..9789625,5	K562	blood:
9	chr2:9696523..9698235-chr2:9781544..9783668,2	K562	blood:
10	chr2:9769023..9772880-chr2:9783334..9787114,8	MCF-7	breast:
11	chr2:9782904..9785147-chr2:9789937..9793084,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000240687	Chromatin interaction
ENSG00000134308	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10427360	0.92[ASN][1000 genomes]
rs10495569	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12620485	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1806668	0.97[ASN][1000 genomes]
rs1976902	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs2091210	1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs3762535	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs4145375	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs4668626	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs4669402	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4669403	0.92[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs4669404	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56068986	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6432026	0.91[ASN][1000 genomes]
rs6432027	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6715748	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs6732745	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs73913149	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73913150	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73913152	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7567578	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv580915	chr2:9308148-9844178	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv1011802	chr2:9766171-9808284	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv518363	chr2:9777229-9788315	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9778800-9783800	Weak transcription	Esophagus	oesophagus
2	chr2:9778800-9783800	Weak transcription	Pancreas	Pancrea
3	chr2:9778800-9784000	Weak transcription	Fetal Intestine Large	intestine
4	chr2:9778800-9788400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:9779400-9784800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:9779400-9786400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:9779600-9789400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:9779800-9784400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:9779800-9784400	Weak transcription	Fetal Intestine Small	intestine
10	chr2:9780000-9786400	Weak transcription	HSMMtube	muscle
11	chr2:9780200-9786400	Weak transcription	Lung	lung
12	chr2:9780200-9786400	Weak transcription	HSMM	muscle
13	chr2:9780400-9783800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:9780400-9785200	Weak transcription	Fetal Lung	lung
15	chr2:9780800-9788000	Weak transcription	Fetal Heart	heart
16	chr2:9781000-9783800	Weak transcription	NHEK	skin
17	chr2:9781000-9784600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:9781000-9785400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:9781000-9785400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:9781000-9786400	Weak transcription	Ovary	ovary
21	chr2:9781200-9783800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:9782200-9784000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:9782600-9783800	Enhancers	Primary B cells from peripheral blood	blood
24	chr2:9782800-9784200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:9783000-9784600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:9783000-9786400	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:9783000-9786600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:9783200-9784200	Weak transcription	HMEC	breast
29	chr2:9783200-9784800	Weak transcription	Placenta	Placenta
30	chr2:9783200-9786400	Weak transcription	Brain Angular Gyrus	brain
31	chr2:9783200-9788400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:9783200-9789200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:9783400-9783800	Weak transcription	Brain Substantia Nigra	brain
34	chr2:9783600-9783800	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr2:9783600-9783800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
36	chr2:9783600-9785000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links