Variant report

Variant	rs1553010
Chromosome Location	chr13:97997538-97997539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:97984606..97986833-chr13:97996758..97998776,2	MCF-7	breast:
2	chr13:97992068..97993792-chr13:97995269..97997609,2	K562	blood:
3	chr13:97990074..97993792-chr13:97995202..97997609,3	K562	blood:
4	chr13:97873255..97877667-chr13:97995725..97999386,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139793	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11618766	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11839205	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs11843522	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs1553011	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17301432	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3782984	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs3782986	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap]
rs59101263	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59190871	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs66473447	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7992346	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs875104	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9513238	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9516905	0.86[MEX][hapmap]
rs9516909	0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9516912	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9516916	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs9582128	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap]
rs9584552	0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap]
rs9584563	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs9584565	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]

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	nsv832694	chr13:97930561-98137882	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1553010	DZIP1	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:97981000-97998800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr13:97982000-98002200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr13:97982000-98009000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:97982600-98020800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr13:97984000-98000800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr13:97986200-98003200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr13:97986600-97998400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr13:97989200-97999000	Weak transcription	Colonic Mucosa	Colon
9	chr13:97989400-97999200	Weak transcription	NH-A	brain
10	chr13:97989600-97998600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr13:97989600-97999400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr13:97990000-97998600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr13:97991200-97998800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:97991400-98002600	Weak transcription	Fetal Brain Female	brain
15	chr13:97991600-97998800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr13:97991600-97999000	Weak transcription	Spleen	Spleen
17	chr13:97991600-97999600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr13:97991600-98020800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr13:97991800-97998600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr13:97991800-97999000	Weak transcription	Esophagus	oesophagus
21	chr13:97991800-98001000	Weak transcription	Fetal Brain Male	brain
22	chr13:97992000-97998400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr13:97992000-97998800	Weak transcription	Gastric	stomach
24	chr13:97992000-98006200	Weak transcription	Psoas Muscle	Psoas
25	chr13:97992200-97999200	Weak transcription	Aorta	Aorta
26	chr13:97992400-97998800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr13:97992400-97998800	Weak transcription	Pancreas	Pancrea
28	chr13:97992400-97999000	Weak transcription	Right Ventricle	heart
29	chr13:97992400-97999400	Weak transcription	HSMMtube	muscle
30	chr13:97992600-97999000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr13:97992800-98001000	Weak transcription	HSMM	muscle
32	chr13:97992800-98020800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr13:97993200-97999800	Weak transcription	Fetal Kidney	kidney
34	chr13:97993600-97999000	Weak transcription	NHEK	skin
35	chr13:97994000-97998200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr13:97994000-97998800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr13:97994200-98016200	Weak transcription	NHDF-Ad	bronchial
38	chr13:97995000-97997600	Genic enhancers	HUVEC	blood vessel
39	chr13:97995000-98007400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr13:97995200-97997600	Strong transcription	K562	blood
41	chr13:97995200-98007400	Strong transcription	Primary T cells from cord blood	blood
42	chr13:97995200-98007800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr13:97995200-98011000	Strong transcription	Placenta	Placenta
44	chr13:97995400-98050200	Weak transcription	Small Intestine	intestine
45	chr13:97995600-97997600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr13:97995600-98005600	Strong transcription	Hela-S3	cervix
47	chr13:97995800-97998400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr13:97996000-97998400	Enhancers	Brain Hippocampus Middle	brain
49	chr13:97996000-97998600	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr13:97996000-97998800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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