Variant report

Variant	rs7559738
Chromosome Location	chr2:86741044-86741045
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86665985..86667815-chr2:86739595..86741738,2	K562	blood:
2	chr2:86739689..86741433-chr2:86750105..86753068,2	MCF-7	breast:
3	chr2:86735334..86737957-chr2:86740188..86742060,2	K562	blood:

Variant related genes	Relation type
ENSG00000115548	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11127039	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11687775	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883727	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890049	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11894098	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11897930	0.87[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55647305	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56184319	0.85[EUR][1000 genomes]
rs6755535	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67847575	0.84[EUR][1000 genomes]
rs67897621	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72930333	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72932325	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590671	1.00[JPT][hapmap]
rs7598175	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7600791	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:86726400-86741800	Weak transcription	NH-A	brain
3	chr2:86726400-86753000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:86726600-86748600	Weak transcription	Hela-S3	cervix
5	chr2:86728200-86755800	Weak transcription	Fetal Brain Male	brain
6	chr2:86728400-86747200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:86729000-86747000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:86732400-86745000	Weak transcription	Fetal Kidney	kidney
9	chr2:86733000-86759400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:86733400-86758600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:86734000-86784800	Weak transcription	Osteobl	bone
12	chr2:86736400-86770600	Weak transcription	Brain Angular Gyrus	brain
13	chr2:86736800-86754400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:86737000-86743600	Weak transcription	Fetal Brain Female	brain
15	chr2:86737000-86747200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:86737000-86752600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr2:86737000-86753000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:86737000-86754400	Weak transcription	NHDF-Ad	bronchial
19	chr2:86737000-86761200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:86737000-86772800	Weak transcription	Pancreas	Pancrea
21	chr2:86737200-86741400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:86737200-86745400	Weak transcription	Brain Anterior Caudate	brain
23	chr2:86737200-86746200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:86737200-86746600	Weak transcription	GM12878-XiMat	blood
25	chr2:86737200-86746800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:86737200-86747000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:86737200-86747400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:86737200-86747600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:86737200-86751600	Weak transcription	HSMM	muscle
30	chr2:86737400-86747400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:86737400-86747400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:86737400-86747400	Weak transcription	Esophagus	oesophagus
33	chr2:86737400-86749000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:86737400-86753000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:86737400-86755400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:86737400-86756800	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:86737400-86757400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:86737400-86788400	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:86737600-86742200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr2:86737600-86745600	Weak transcription	Fetal Stomach	stomach
41	chr2:86737600-86746200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:86737600-86746600	Weak transcription	NHLF	lung
43	chr2:86737600-86747000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:86737600-86747200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:86737600-86747400	Weak transcription	Adipose Nuclei	Adipose
46	chr2:86737600-86747800	Weak transcription	Gastric	stomach
47	chr2:86737600-86748800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:86737600-86768400	Weak transcription	Ovary	ovary
49	chr2:86737800-86747200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:86737800-86747200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links