Variant report

Variant	rs202085
Chromosome Location	chr13:30805266-30805267
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30796832..30799585-chr13:30801538..30805408,3	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1099846	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1099848	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs169332	0.82[ASN][1000 genomes]
rs175730	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1964165	0.89[EUR][1000 genomes]
rs202094	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202095	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202096	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202112	0.83[EUR][1000 genomes]
rs202113	0.91[EUR][1000 genomes]
rs202114	0.91[EUR][1000 genomes]
rs594411	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs605095	0.82[ASN][1000 genomes]
rs648538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs652053	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs666245	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs674253	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs846486	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs846488	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs861727	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832572	chr13:30650005-30835256	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv528192	chr13:30800293-30805992	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs202085	KATNAL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30765600-30807000	Weak transcription	Gastric	stomach
2	chr13:30774400-30812600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr13:30790000-30807000	Weak transcription	Small Intestine	intestine
4	chr13:30791000-30807200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr13:30791000-30808800	Weak transcription	Brain Hippocampus Middle	brain
6	chr13:30791000-30811600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr13:30791000-30831400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr13:30795800-30805600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr13:30796600-30807000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr13:30796600-30808600	Weak transcription	Brain Substantia Nigra	brain
11	chr13:30796800-30831400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr13:30797000-30808600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr13:30797000-30823400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr13:30797800-30814800	Weak transcription	Placenta	Placenta
15	chr13:30798800-30810800	Strong transcription	Fetal Thymus	thymus
16	chr13:30799000-30805600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr13:30799200-30805600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr13:30799200-30805600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr13:30799200-30805600	Strong transcription	Liver	Liver
20	chr13:30799200-30805600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr13:30799200-30811800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr13:30799200-30831400	Weak transcription	Aorta	Aorta
23	chr13:30799400-30805400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr13:30799400-30805600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr13:30799400-30805600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr13:30799400-30805600	Strong transcription	Fetal Lung	lung
27	chr13:30799400-30805800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr13:30799400-30805800	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr13:30799400-30808600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr13:30799400-30809000	Weak transcription	HSMMtube	muscle
31	chr13:30799400-30812400	Weak transcription	Fetal Kidney	kidney
32	chr13:30799400-30814200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr13:30799400-30814400	Weak transcription	Brain Angular Gyrus	brain
34	chr13:30799400-30814400	Weak transcription	HepG2	liver
35	chr13:30799400-30823200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr13:30799400-30831600	Weak transcription	Right Ventricle	heart
37	chr13:30799600-30805600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr13:30799600-30805600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr13:30799600-30805800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr13:30799600-30807600	Weak transcription	Psoas Muscle	Psoas
41	chr13:30799600-30810400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr13:30799600-30817400	Weak transcription	Brain Anterior Caudate	brain
43	chr13:30799600-30823400	Weak transcription	A549	lung
44	chr13:30799600-30823400	Weak transcription	NHEK	skin
45	chr13:30799600-30845200	Weak transcription	HMEC	breast
46	chr13:30799800-30810800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr13:30800000-30805600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr13:30800200-30805600	Strong transcription	Stomach Smooth Muscle	stomach
49	chr13:30800200-30806000	Strong transcription	Primary B cells from cord blood	blood
50	chr13:30800400-30805400	Strong transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links