Variant report

Variant	rs6733426
Chromosome Location	chr2:180830958-180830959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180828855..180831224-chr2:180831279..180833933,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12465592	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12468986	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12693214	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12693215	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16867131	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1904850	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2367990	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs259810	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs259811	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2678936	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3843323	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3845701	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3856415	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56401468	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6433816	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6433818	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6433820	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6433821	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6722147	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6727890	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6744281	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6759271	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72958863	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72960660	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72960664	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72960701	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72962517	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72962575	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs818661	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9288045	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875472	chr2:180696414-181024926	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv875473	chr2:180696414-181055597	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv521134	chr2:180746041-180848488	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1006598	chr2:180766983-180923051	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv531444	chr2:180796233-181434590	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180801000-180836400	Weak transcription	Psoas Muscle	Psoas
2	chr2:180803400-180843600	Weak transcription	Fetal Brain Male	brain
3	chr2:180805600-180831800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:180807000-180858400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:180808200-180840000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr2:180808200-180860400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:180808600-180831400	Strong transcription	Primary B cells from peripheral blood	blood
8	chr2:180809000-180856000	Weak transcription	Fetal Stomach	stomach
9	chr2:180809400-180871000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:180811200-180856200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:180813400-180868200	Weak transcription	Stomach Mucosa	stomach
12	chr2:180813800-180831800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:180816600-180847200	Weak transcription	Hela-S3	cervix
14	chr2:180816800-180832000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:180816800-180835400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:180816800-180841800	Weak transcription	Small Intestine	intestine
17	chr2:180816800-180852800	Weak transcription	Lung	lung
18	chr2:180816800-180860400	Weak transcription	Right Ventricle	heart
19	chr2:180816800-180868400	Weak transcription	Pancreas	Pancrea
20	chr2:180816800-180869000	Weak transcription	Spleen	Spleen
21	chr2:180816800-180870600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:180817200-180860400	Weak transcription	Aorta	Aorta
23	chr2:180817200-180860400	Weak transcription	Gastric	stomach
24	chr2:180817800-180848400	Weak transcription	NHLF	lung
25	chr2:180819000-180834600	Weak transcription	Brain Substantia Nigra	brain
26	chr2:180819000-180845800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:180819000-180871000	Weak transcription	Esophagus	oesophagus
28	chr2:180819200-180844400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:180819600-180832000	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:180819600-180843800	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:180819800-180834800	Weak transcription	Colonic Mucosa	Colon
32	chr2:180820400-180831800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:180821600-180858800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr2:180821800-180831000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:180822000-180832000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr2:180822000-180839200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:180822000-180853600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:180822200-180831000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:180822200-180832000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:180822200-180838400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:180822200-180858200	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr2:180822400-180836800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr2:180822400-180838600	Strong transcription	Liver	Liver
44	chr2:180822800-180834200	Weak transcription	Brain Germinal Matrix	brain
45	chr2:180823200-180831000	Strong transcription	Placenta	Placenta
46	chr2:180823400-180870600	Weak transcription	Fetal Intestine Small	intestine
47	chr2:180824400-180831000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:180824400-180832800	Strong transcription	HSMM	muscle
49	chr2:180825400-180832800	Strong transcription	Primary B cells from cord blood	blood
50	chr2:180825600-180832200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links