Variant report

Variant	rs62203669
Chromosome Location	chr2:211335543-211335544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:211332522..211338097-chr2:211338673..211343444,12	K562	blood:
2	chr2:211334411..211336999-chr2:211341944..211344894,2	K562	blood:
3	chr2:211333118..211336164-chr2:211339980..211343181,4	MCF-7	breast:
4	chr2:211331221..211336571-chr2:211337651..211341435,6	K562	blood:

Variant related genes	Relation type
ENSG00000021826	Chromatin interaction
ENSG00000115365	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10932334	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12464878	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12474078	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12618926	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12623942	0.98[ASN][1000 genomes]
rs1396954	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17552879	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2042049	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287417	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287418	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287419	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2287420	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2287421	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2287422	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2370948	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3732055	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3755182	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770685	0.99[ASN][1000 genomes]
rs3770687	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3770690	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770691	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3856340	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3856342	1.00[ASN][1000 genomes]
rs3856343	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3856344	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856345	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856346	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856347	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856348	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856349	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4672575	0.94[ASN][1000 genomes]
rs4672577	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4673530	0.99[ASN][1000 genomes]
rs4673531	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4673532	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4673533	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62203668	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62203670	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62203672	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62203673	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62203674	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62203675	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6727682	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7569252	0.82[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	esv3398091	chr2:211315261-211634200	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs62203669	LANCL1	Cis_1M	lymphoblastoid	RTeQTL
rs62203669	CPS1	cis	Adipose Subcutaneous	GTEx
rs62203669	CPS1	cis	lung	GTEx
rs62203669	CPS1	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211295000-211336000	Weak transcription	Colonic Mucosa	Colon
2	chr2:211295000-211340600	Weak transcription	HUVEC	blood vessel
3	chr2:211296000-211340200	Weak transcription	Small Intestine	intestine
4	chr2:211296400-211341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:211297800-211336200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:211301200-211340200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:211301200-211340600	Weak transcription	Fetal Intestine Small	intestine
8	chr2:211301200-211340800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:211301400-211336000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:211315400-211340000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:211315600-211337800	Strong transcription	Fetal Thymus	thymus
12	chr2:211315600-211339600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:211315800-211337200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:211315800-211337800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:211316000-211338000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:211316200-211337800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:211316200-211337800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:211316600-211339000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:211316800-211338800	Strong transcription	Dnd41	blood
20	chr2:211318000-211337800	Strong transcription	Stomach Smooth Muscle	stomach
21	chr2:211321200-211337600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:211322400-211340400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:211322600-211340400	Weak transcription	K562	blood
24	chr2:211323400-211336000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:211323400-211340200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:211324200-211336000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:211324800-211339000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:211325800-211340800	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:211326800-211338800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:211326800-211339800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr2:211327200-211338000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr2:211327400-211339000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:211327600-211339000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:211328200-211337800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:211328600-211337000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr2:211329400-211336600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:211329600-211336800	Strong transcription	Left Ventricle	heart
38	chr2:211329600-211337200	Strong transcription	Primary T cells from cord blood	blood
39	chr2:211329800-211336400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:211329800-211336400	Strong transcription	Brain Cingulate Gyrus	brain
41	chr2:211329800-211336800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:211329800-211336800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr2:211329800-211336800	Strong transcription	Adipose Nuclei	Adipose
44	chr2:211329800-211336800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:211329800-211336800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr2:211329800-211336800	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:211329800-211336800	Strong transcription	A549	lung
48	chr2:211329800-211337000	Strong transcription	Primary B cells from cord blood	blood
49	chr2:211329800-211337200	Strong transcription	Liver	Liver
50	chr2:211329800-211338000	Strong transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links