Variant report

Variant	rs2285720
Chromosome Location	chr4:106083776-106083777
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:106080873..106083854-chr4:106094011..106096644,2	MCF-7	breast:
2	chr4:106082088..106084458-chr4:106094804..106097653,2	K562	blood:
3	chr4:106066858..106068608-chr4:106083619..106085703,2	K562	blood:
4	chr4:106066054..106072074-chr4:106082791..106088077,10	MCF-7	breast:
5	chr4:106083619..106085487-chr4:106089285..106091911,2	K562	blood:

Variant related genes	Relation type
ENSG00000168769	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10010281	0.80[YRI][hapmap]
rs10014102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10022109	1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[ASN][1000 genomes]
rs12641113	1.00[ASN][1000 genomes]
rs12643257	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12645165	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12647922	0.81[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[YRI][hapmap];0.85[ASN][1000 genomes]
rs1391440	0.86[JPT][hapmap]
rs17583558	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs17617028	1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[ASN][1000 genomes]
rs2189234	0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs28493806	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2903386	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62331150	0.81[ASN][1000 genomes]
rs62331151	0.92[ASN][1000 genomes]
rs974801	0.96[CEU][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9790517	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs9884482	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2285720	PPA2	cis	cerebellum	SCAN
rs2285720	NPNT	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106069400-106087600	Weak transcription	Lung	lung
2	chr4:106069400-106114200	Weak transcription	Esophagus	oesophagus
3	chr4:106069600-106102400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:106069800-106101000	Weak transcription	HSMM	muscle
5	chr4:106069800-106101800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:106070400-106107800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:106070400-106111600	Weak transcription	Placenta	Placenta
8	chr4:106071000-106100800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:106071800-106084400	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:106072600-106100600	Weak transcription	Adipose Nuclei	Adipose
11	chr4:106076000-106084400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr4:106076200-106089200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:106076200-106092800	Weak transcription	Psoas Muscle	Psoas
14	chr4:106076200-106093000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:106077000-106100800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:106077000-106112000	Weak transcription	Aorta	Aorta
17	chr4:106078000-106092200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:106078000-106112800	Weak transcription	Fetal Kidney	kidney
19	chr4:106080200-106085200	Weak transcription	Primary B cells from cord blood	blood
20	chr4:106080200-106091400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr4:106080400-106088800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr4:106080400-106088800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:106080600-106086400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr4:106080600-106101800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:106080600-106102800	Weak transcription	NHEK	skin
26	chr4:106080600-106105800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:106080600-106107800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:106080800-106085600	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr4:106080800-106085800	Weak transcription	Left Ventricle	heart
30	chr4:106080800-106091000	Weak transcription	Ovary	ovary
31	chr4:106080800-106095200	Weak transcription	Fetal Intestine Large	intestine
32	chr4:106081000-106087000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr4:106081000-106089400	Weak transcription	Fetal Intestine Small	intestine
34	chr4:106082400-106084000	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr4:106082800-106083800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr4:106082800-106083800	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr4:106082800-106084600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:106083000-106084200	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr4:106083000-106086200	Enhancers	Fetal Heart	heart
40	chr4:106083200-106083800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:106083200-106083800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:106083200-106083800	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr4:106083200-106083800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:106083200-106083800	Enhancers	Brain Anterior Caudate	brain
45	chr4:106083200-106083800	Enhancers	Brain Substantia Nigra	brain
46	chr4:106083200-106083800	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr4:106083200-106083800	Enhancers	Fetal Muscle Leg	muscle
48	chr4:106083200-106083800	Enhancers	Gastric	stomach
49	chr4:106083200-106083800	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr4:106083200-106084000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links