Variant report

Variant	rs10197533
Chromosome Location	chr2:55267153-55267154
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55258298..55260902-chr2:55265959..55268145,3	MCF-7	breast:
2	chr2:55265645..55268025-chr2:55268205..55270605,2	MCF-7	breast:
3	chr2:55257553..55263983-chr2:55266645..55270936,7	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10084445	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10170102	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10175952	1.00[CEU][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10179491	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10180207	0.92[EUR][1000 genomes]
rs10181115	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10182203	0.94[EUR][1000 genomes]
rs10191684	0.82[AMR][1000 genomes]
rs10191748	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs10191774	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10198096	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10206953	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10207701	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11125554	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13385999	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[AMR][1000 genomes]
rs13387710	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13394823	0.82[AMR][1000 genomes]
rs13394824	0.82[AMR][1000 genomes]
rs13400353	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13401780	0.86[EUR][1000 genomes]
rs13416852	0.83[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs17046567	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17046569	1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4358163	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes]
rs60989108	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6545469	0.84[ASW][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6545470	0.86[EUR][1000 genomes]
rs6715980	1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes]
rs6725187	0.82[AMR][1000 genomes]
rs6744637	0.84[ASW][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs6758258	0.80[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs6760773	0.84[EUR][1000 genomes]
rs72912579	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7570298	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7584992	0.80[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs7592869	0.86[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

No data

Chromatin state (count:95 , 50 per page) page: 1 2

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	chr2:55250400-55271000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:55250400-55274000	Weak transcription	Pancreas	Pancrea
5	chr2:55253400-55273000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:55254200-55269800	Weak transcription	Aorta	Aorta
7	chr2:55254200-55270400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:55255400-55272600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:55255400-55272600	Weak transcription	Fetal Intestine Small	intestine
10	chr2:55256400-55270400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:55259000-55267400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:55259000-55272800	Weak transcription	Small Intestine	intestine
13	chr2:55259200-55272800	Weak transcription	Fetal Heart	heart
14	chr2:55259400-55275200	Weak transcription	Esophagus	oesophagus
15	chr2:55260800-55270400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:55260800-55271200	Weak transcription	Lung	lung
17	chr2:55260800-55271200	Weak transcription	Right Atrium	heart
18	chr2:55260800-55272000	Weak transcription	NH-A	brain
19	chr2:55260800-55272400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:55260800-55273200	Weak transcription	Psoas Muscle	Psoas
21	chr2:55261200-55273000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:55261400-55272800	Weak transcription	Thymus	Thymus
23	chr2:55261600-55269400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:55261600-55271200	Weak transcription	Ovary	ovary
25	chr2:55262600-55270200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:55262800-55267600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:55263800-55267200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:55264200-55267600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:55264600-55267200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:55264600-55268600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr2:55264800-55267400	Weak transcription	NHLF	lung
32	chr2:55264800-55267600	Weak transcription	HSMMtube	muscle
33	chr2:55264800-55268400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:55264800-55270200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:55264800-55271200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:55265000-55267400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr2:55265000-55267600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:55265000-55267600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:55265000-55268400	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:55265000-55270400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:55265600-55267200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:55265600-55267200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:55265600-55270400	Enhancers	Brain Hippocampus Middle	brain
44	chr2:55265800-55267200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:55266200-55267200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:55266200-55267400	Weak transcription	Adipose Nuclei	Adipose
47	chr2:55266200-55267400	Weak transcription	Brain Germinal Matrix	brain
48	chr2:55266200-55267600	Weak transcription	Primary T cells from cord blood	blood
49	chr2:55266200-55267600	Weak transcription	Brain Substantia Nigra	brain
50	chr2:55266200-55268400	Weak transcription	HSMM	muscle

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