Variant report

Variant	rs2936052
Chromosome Location	chr1:222802376-222802377
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222801864..222803416-chr1:222815988..222818056,2	K562	blood:

Variant related genes	Relation type
ENSG00000154305	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11485123	0.81[EUR][1000 genomes]
rs1391557	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1391558	0.92[EUR][1000 genomes]
rs1498382	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17011666	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1909195	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1909197	0.81[AMR][1000 genomes]
rs2030076	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2088514	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2133188	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2270707	0.80[AMR][1000 genomes]
rs2378604	0.82[EUR][1000 genomes]
rs2936020	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2936023	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2936049	0.90[EUR][1000 genomes]
rs2936051	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2936054	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3002145	0.80[EUR][1000 genomes]
rs3002146	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3002148	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3008614	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3008615	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3008616	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3008618	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3008621	0.80[EUR][1000 genomes]
rs3008622	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3008625	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3008629	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3008637	0.90[EUR][1000 genomes]
rs34433664	0.83[EUR][1000 genomes]
rs3811465	0.83[EUR][1000 genomes]
rs61827168	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9441835	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9441926	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	esv3351619	chr1:222801947-222802386	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222792400-222816600	Weak transcription	Small Intestine	intestine
2	chr1:222792600-222816600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:222792600-222817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:222793200-222802800	Weak transcription	Gastric	stomach
5	chr1:222793200-222816600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:222793200-222816600	Weak transcription	Hela-S3	cervix
7	chr1:222793600-222816600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:222794000-222806800	Strong transcription	Primary T cells from cord blood	blood
9	chr1:222794200-222802600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:222794200-222805000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:222794600-222803600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:222794600-222807200	Strong transcription	Fetal Thymus	thymus
13	chr1:222794600-222809800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:222794600-222810400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:222794600-222810400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:222794600-222813400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:222794600-222813600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:222794600-222814000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:222794600-222815000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:222794800-222803800	Strong transcription	Primary B cells from peripheral blood	blood
21	chr1:222794800-222804000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr1:222794800-222813200	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:222794800-222813600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:222795200-222807000	Strong transcription	HepG2	liver
25	chr1:222795200-222807600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr1:222795200-222807600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr1:222795200-222807800	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:222795400-222806600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:222795400-222806800	Strong transcription	Stomach Smooth Muscle	stomach
30	chr1:222795400-222807200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr1:222795400-222807600	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:222795400-222810400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:222795400-222810600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:222795400-222810600	Strong transcription	Fetal Muscle Leg	muscle
35	chr1:222795400-222812000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr1:222795400-222813400	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:222795600-222803000	Strong transcription	Primary hematopoietic stem cells	blood
38	chr1:222795600-222804000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:222795600-222807200	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr1:222795600-222807200	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:222795600-222810600	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:222795800-222802400	Weak transcription	Psoas Muscle	Psoas
43	chr1:222795800-222803200	Strong transcription	Brain Anterior Caudate	brain
44	chr1:222795800-222810600	Strong transcription	Adipose Nuclei	Adipose
45	chr1:222796000-222807600	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:222796200-222807800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:222797000-222809200	Strong transcription	Fetal Intestine Large	intestine
48	chr1:222797000-222812400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr1:222797400-222803200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:222797400-222807000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links