Variant report

Variant	rs10173203
Chromosome Location	chr2:55258704-55258705
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55255815..55260220-chr2:55273453..55278520,8	MCF-7	breast:
2	chr2:55252582..55260799-chr2:55274165..55279100,17	MCF-7	breast:
3	chr2:55257553..55263983-chr2:55266645..55270936,7	K562	blood:
4	chr2:55255745..55260236-chr2:55263069..55266549,5	K562	blood:
5	chr2:55258298..55260902-chr2:55265959..55268145,3	MCF-7	breast:
6	chr2:55257154..55258943-chr2:55260166..55262885,2	K562	blood:
7	chr2:55258610..55260236-chr2:55264059..55265743,2	K562	blood:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10084445	0.96[YRI][hapmap]
rs10189094	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs11125554	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs13385999	0.86[LWK][hapmap]
rs13387836	0.87[EUR][1000 genomes]
rs17046567	0.96[YRI][hapmap]
rs17046569	0.97[LWK][hapmap];0.96[YRI][hapmap]
rs3198123	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3806572	0.90[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6705519	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6757907	0.83[CEU][hapmap]
rs6760379	0.87[EUR][1000 genomes]
rs7601895	0.83[CEU][hapmap];0.88[EUR][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	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10173203	VRK2	cis	cerebellum	SCAN
rs10173203	TSPYL6	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
2	chr2:55241000-55272400	Weak transcription	Fetal Kidney	kidney
3	chr2:55243000-55262400	Weak transcription	Hela-S3	cervix
4	chr2:55243800-55259800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:55245600-55265600	Weak transcription	Stomach Mucosa	stomach
6	chr2:55246800-55259800	Weak transcription	NH-A	brain
7	chr2:55248200-55259200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:55250000-55260000	Weak transcription	Gastric	stomach
9	chr2:55250400-55271000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:55250400-55274000	Weak transcription	Pancreas	Pancrea
11	chr2:55251400-55259400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr2:55252400-55259000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr2:55252600-55261400	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr2:55253400-55273000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:55253800-55260400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr2:55253800-55260600	Weak transcription	Right Atrium	heart
17	chr2:55253800-55261400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:55254200-55269800	Weak transcription	Aorta	Aorta
19	chr2:55254200-55270400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:55254400-55262600	Enhancers	Brain Hippocampus Middle	brain
21	chr2:55254600-55258800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr2:55254600-55259800	Weak transcription	Primary B cells from cord blood	blood
23	chr2:55254600-55259800	Weak transcription	Thymus	Thymus
24	chr2:55254600-55260000	Weak transcription	Fetal Thymus	thymus
25	chr2:55254600-55260600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:55254800-55260000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:55254800-55260400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:55254800-55265000	Enhancers	Brain Substantia Nigra	brain
29	chr2:55255000-55259400	Enhancers	Muscle Satellite Cultured Cells	--
30	chr2:55255000-55260600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr2:55255200-55261200	Weak transcription	HUVEC	blood vessel
32	chr2:55255400-55259800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:55255400-55259800	Weak transcription	Dnd41	blood
34	chr2:55255400-55260000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:55255400-55260400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr2:55255400-55272600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:55255400-55272600	Weak transcription	Fetal Intestine Small	intestine
38	chr2:55256000-55260200	Weak transcription	Primary T cells from cord blood	blood
39	chr2:55256000-55260200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:55256000-55260200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:55256200-55260000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr2:55256400-55266600	Weak transcription	Left Ventricle	heart
43	chr2:55256400-55270400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr2:55256600-55259000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr2:55256600-55259800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr2:55256600-55260200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr2:55256600-55262200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:55256600-55264000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:55256600-55265200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:55256800-55260400	Weak transcription	HepG2	liver

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