Variant report

Variant	rs56888009
Chromosome Location	chr3:136412703-136412704
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136405715..136407497-chr3:136411173..136412850,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10513016	0.96[EUR][1000 genomes]
rs16844056	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17365351	0.96[EUR][1000 genomes]
rs17466223	0.96[EUR][1000 genomes]
rs55763637	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57466072	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57681357	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58636237	0.83[EUR][1000 genomes]
rs59361983	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59616231	0.96[EUR][1000 genomes]
rs59696368	0.96[EUR][1000 genomes]
rs66470158	0.90[EUR][1000 genomes]
rs66471262	0.96[EUR][1000 genomes]
rs66637228	0.97[EUR][1000 genomes]
rs66739346	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66902780	0.90[EUR][1000 genomes]
rs67231188	0.94[EUR][1000 genomes]
rs67236827	0.96[EUR][1000 genomes]
rs67281610	0.82[EUR][1000 genomes]
rs67303976	0.82[EUR][1000 genomes]
rs67546863	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773495	0.82[EUR][1000 genomes]
rs67888773	0.90[EUR][1000 genomes]
rs67902591	0.83[EUR][1000 genomes]
rs67923745	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68018658	0.97[EUR][1000 genomes]
rs6805814	1.00[ASN][1000 genomes]
rs72975363	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228025	0.87[EUR][1000 genomes]
rs73228037	0.90[EUR][1000 genomes]
rs73228040	0.90[EUR][1000 genomes]
rs73230052	0.90[EUR][1000 genomes]
rs73230065	1.00[ASN][1000 genomes]
rs73230077	0.83[EUR][1000 genomes]
rs73230078	0.83[EUR][1000 genomes]
rs73230095	0.82[EUR][1000 genomes]
rs7636806	0.82[EUR][1000 genomes]
rs7646563	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7646723	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs923001	0.96[EUR][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	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1008866	chr3:136364511-136427790	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136386400-136412800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:136390200-136413000	Weak transcription	Pancreas	Pancrea
3	chr3:136390800-136447800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:136395000-136418200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:136405400-136413000	Weak transcription	Fetal Heart	heart
6	chr3:136408800-136414600	Weak transcription	Gastric	stomach
7	chr3:136409400-136413000	Weak transcription	Adipose Nuclei	Adipose
8	chr3:136409400-136417800	Weak transcription	Aorta	Aorta
9	chr3:136409400-136422000	Weak transcription	Lung	lung
10	chr3:136410000-136413400	Enhancers	K562	blood
11	chr3:136410600-136414800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:136411000-136414200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:136411000-136415600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
14	chr3:136411000-136416200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:136411000-136444400	Weak transcription	Fetal Lung	lung
16	chr3:136411200-136415000	Weak transcription	NHDF-Ad	bronchial
17	chr3:136411400-136416800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:136411400-136417800	Weak transcription	Left Ventricle	heart
19	chr3:136411600-136413400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
20	chr3:136411600-136413600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:136411600-136416400	ZNF genes & repeats	Dnd41	blood
22	chr3:136411600-136419200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:136411600-136427800	Weak transcription	Right Ventricle	heart
24	chr3:136411800-136413800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
25	chr3:136411800-136415000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:136411800-136415000	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:136411800-136416400	ZNF genes & repeats	Primary T cells from cord blood	blood
28	chr3:136411800-136417000	Weak transcription	Brain Substantia Nigra	brain
29	chr3:136412000-136413000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr3:136412000-136413200	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr3:136412000-136413200	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
32	chr3:136412000-136415200	ZNF genes & repeats	Thymus	Thymus
33	chr3:136412000-136415400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
34	chr3:136412000-136415400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr3:136412000-136416200	ZNF genes & repeats	Primary B cells from cord blood	blood
36	chr3:136412200-136413200	Strong transcription	Fetal Muscle Leg	muscle
37	chr3:136412400-136413200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:136412400-136413200	Enhancers	Right Atrium	heart
39	chr3:136412400-136413600	ZNF genes & repeats	Fetal Intestine Small	intestine
40	chr3:136412400-136414400	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr3:136412600-136412800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:136412600-136413000	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:136412600-136413400	Enhancers	Psoas Muscle	Psoas
44	chr3:136412600-136413600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
45	chr3:136412600-136414200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:136412600-136415000	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr3:136412600-136416200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links