Variant report

Variant	rs552989
Chromosome Location	chr9:101137895-101137896
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:101135309..101137051-chr9:101137273..101139774,2	K562	blood:
2	chr9:101137194..101138709-chr9:101140809..101142702,2	K562	blood:
3	chr9:101136620..101139249-chr9:101156990..101158557,2	K562	blood:
4	chr9:101125220..101129376-chr9:101135603..101141784,6	K562	blood:
5	chr9:101127682..101131370-chr9:101135028..101139404,5	K562	blood:
6	chr9:101137064..101139135-chr9:101558434..101560859,2	K562	blood:
7	chr9:101135309..101136944-chr9:101137021..101138773,2	K562	blood:
8	chr9:101102112..101103704-chr9:101137031..101138837,2	K562	blood:
9	chr9:101125471..101127480-chr9:101134828..101138522,3	K562	blood:
10	chr9:101131978..101133928-chr9:101135656..101138427,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000165138	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10818828	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs10818832	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs10818833	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs10986039	0.86[ASN][1000 genomes]
rs10986041	0.86[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs10986044	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs10986060	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs10986062	0.87[CHD][hapmap]
rs2572364	0.85[JPT][hapmap]
rs487910	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs514993	0.82[GIH][hapmap]
rs531529	0.85[JPT][hapmap]
rs553139	0.88[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs567931	0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs583115	1.00[CEU][hapmap]
rs585325	0.85[JPT][hapmap]
rs585819	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs613308	0.85[JPT][hapmap]
rs628997	0.85[JPT][hapmap]
rs644842	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs648085	0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs659768	0.85[JPT][hapmap]
rs660148	0.85[JPT][hapmap]
rs661105	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs661532	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs669095	0.85[JPT][hapmap]
rs774334	0.85[JPT][hapmap]
rs774335	0.85[JPT][hapmap]

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	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831664	chr9:101024862-101205637	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101126600-101142600	Weak transcription	Brain Angular Gyrus	brain
2	chr9:101128200-101164200	Weak transcription	Brain Germinal Matrix	brain
3	chr9:101129000-101156000	Weak transcription	Fetal Brain Female	brain
4	chr9:101132800-101142800	Weak transcription	Right Atrium	heart
5	chr9:101133400-101138000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr9:101133400-101139400	Enhancers	Pancreas	Pancrea
7	chr9:101133400-101142400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:101134200-101142600	Enhancers	Fetal Intestine Large	intestine
9	chr9:101134400-101142400	Enhancers	Fetal Intestine Small	intestine
10	chr9:101134600-101139400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:101134800-101140000	Weak transcription	Spleen	Spleen
12	chr9:101134800-101142400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:101134800-101143000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:101135200-101138400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:101135600-101138200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:101135800-101138000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:101135800-101138000	Enhancers	NHLF	lung
18	chr9:101135800-101138200	Enhancers	HUVEC	blood vessel
19	chr9:101135800-101140000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr9:101136000-101138400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:101136400-101138000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:101136600-101138000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:101136600-101138000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr9:101136800-101138200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:101136800-101144600	Enhancers	Primary B cells from peripheral blood	blood
26	chr9:101137000-101145000	Enhancers	Primary B cells from cord blood	blood
27	chr9:101137400-101138000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr9:101137400-101138200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:101137400-101138600	Enhancers	NHDF-Ad	bronchial
30	chr9:101137400-101142200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr9:101137400-101142200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:101137400-101142400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:101137600-101138200	Enhancers	NH-A	brain
34	chr9:101137600-101138400	Enhancers	GM12878-XiMat	blood
35	chr9:101137600-101138400	Enhancers	Osteobl	bone
36	chr9:101137600-101142200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:101137600-101142200	Weak transcription	Fetal Heart	heart
38	chr9:101137600-101142400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr9:101137600-101142400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr9:101137800-101138000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr9:101137800-101138000	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr9:101137800-101139400	Enhancers	K562	blood
43	chr9:101137800-101140200	Weak transcription	Placenta	Placenta
44	chr9:101137800-101142200	Weak transcription	A549	lung
45	chr9:101137800-101142400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:101137800-101142400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr9:101137800-101142400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr9:101137800-101142400	Weak transcription	HMEC	breast
49	chr9:101137800-101142400	Weak transcription	HSMM	muscle
50	chr9:101137800-101142400	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links