Variant report

Variant	rs2068659
Chromosome Location	chr3:150090221-150090222
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150081211..150094856-chr3:150124384..150132921,41	MCF-7	breast:
2	chr3:149958153..149960019-chr3:150088312..150090448,2	MCF-7	breast:
3	chr3:150081035..150094397-chr3:150122156..150134666,40	MCF-7	breast:
4	chr3:150089195..150090821-chr3:150265042..150267654,2	MCF-7	breast:
5	chr3:150048454..150052986-chr3:150087441..150091214,5	MCF-7	breast:
6	chr3:149984985..149987053-chr3:150088170..150090479,2	MCF-7	breast:
7	chr3:150082769..150087099-chr3:150088300..150090870,4	K562	blood:
8	chr3:150087821..150092434-chr3:150124349..150127754,6	K562	blood:
9	chr3:150021733..150026576-chr3:150087273..150091284,6	MCF-7	breast:
10	chr3:150086784..150089218-chr3:150089694..150091385,2	MCF-7	breast:
11	chr3:150088730..150091158-chr3:150119055..150121644,3	MCF-7	breast:
12	chr3:150086519..150091866-chr3:150093461..150097312,5	K562	blood:
13	chr3:149954498..149958099-chr3:150086943..150091403,7	MCF-7	breast:
14	chr3:150087084..150094553-chr3:150124263..150130094,16	K562	blood:
15	chr3:150087916..150090460-chr3:150152430..150154050,2	K562	blood:
16	chr3:150066022..150069420-chr3:150088814..150091274,3	K562	blood:
17	chr3:150033113..150037399-chr3:150086580..150091176,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000244541	Chromatin interaction
ENSG00000196428	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11706784	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719654	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12054166	0.92[ASN][1000 genomes]
rs13069723	0.84[ASN][1000 genomes]
rs13092207	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13092341	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16862648	0.84[ASN][1000 genomes]
rs33988810	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34192407	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34384576	0.85[ASN][1000 genomes]
rs34518530	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34616287	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34991086	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35704634	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35725711	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35982655	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56040746	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62269065	0.84[ASN][1000 genomes]
rs6763024	0.81[ASN][1000 genomes]
rs9682043	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829755	chr3:149992023-150156001	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150086200-150102200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:150088200-150090800	Enhancers	Stomach Mucosa	stomach
3	chr3:150088600-150090400	Enhancers	Colon Smooth Muscle	Colon
4	chr3:150088600-150090800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr3:150088800-150090400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:150088800-150090600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr3:150088800-150090800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr3:150088800-150090800	Enhancers	Fetal Heart	heart
9	chr3:150088800-150093800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:150089000-150090600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:150089000-150090600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:150089400-150090800	Enhancers	HepG2	liver
13	chr3:150089400-150094200	Weak transcription	Small Intestine	intestine
14	chr3:150089600-150090600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr3:150089600-150090600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:150089600-150090600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr3:150089600-150090800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr3:150089600-150094200	Weak transcription	Placenta	Placenta
19	chr3:150089600-150097400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:150089800-150090400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:150089800-150090400	Weak transcription	Psoas Muscle	Psoas
22	chr3:150089800-150090400	Enhancers	K562	blood
23	chr3:150089800-150090600	Enhancers	Fetal Intestine Small	intestine
24	chr3:150089800-150090600	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr3:150089800-150090600	Enhancers	GM12878-XiMat	blood
26	chr3:150089800-150090600	Flanking Active TSS	NHEK	skin
27	chr3:150089800-150090800	Enhancers	Fetal Muscle Leg	muscle
28	chr3:150089800-150090800	Enhancers	Rectal Smooth Muscle	rectum
29	chr3:150089800-150090800	Flanking Active TSS	A549	lung
30	chr3:150089800-150092800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:150089800-150094000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:150089800-150094000	Weak transcription	Brain Germinal Matrix	brain
33	chr3:150089800-150094000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:150089800-150094200	Weak transcription	Left Ventricle	heart
35	chr3:150089800-150094600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:150090000-150090400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:150090000-150090400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:150090000-150090400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr3:150090000-150090400	Enhancers	Liver	Liver
40	chr3:150090000-150090400	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr3:150090000-150090400	Flanking Active TSS	HMEC	breast
42	chr3:150090000-150090800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:150090000-150090800	Enhancers	Adipose Nuclei	Adipose
44	chr3:150090000-150090800	Enhancers	Placenta Amnion	Placenta Amnion
45	chr3:150090000-150090800	Enhancers	Hela-S3	cervix
46	chr3:150090000-150090800	Flanking Active TSS	HUVEC	blood vessel
47	chr3:150090000-150091000	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr3:150090000-150093000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:150090000-150093800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:150090200-150090400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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