Variant report

Variant	rs2378957
Chromosome Location	chr1:185040065-185040066
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	chr1:185039038..185041599-chr1:185124625..185126477,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116668	Chromatin interaction
ENSG00000121486	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1053166	0.90[GIH][hapmap]
rs10911679	0.82[ASW][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap]
rs12063375	0.88[EUR][1000 genomes]
rs12408074	0.95[EUR][1000 genomes]
rs12563135	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs28609768	0.88[ASW][hapmap];0.90[GIH][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs34463352	0.87[EUR][1000 genomes]
rs35507672	0.86[EUR][1000 genomes]
rs3820183	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6677056	0.90[GIH][hapmap];0.86[ASN][1000 genomes]
rs7523448	0.82[ASW][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap]
rs7548237	0.83[GIH][hapmap]
rs950327	0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking 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 miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548396	chr1:185038104-185151378	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185015800-185043400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:185016400-185057000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:185016400-185067200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:185016400-185073800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:185016600-185057000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:185017400-185042800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:185018400-185043000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:185018400-185043200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:185018400-185101800	Weak transcription	Fetal Brain Male	brain
10	chr1:185020600-185040200	Weak transcription	Brain Angular Gyrus	brain
11	chr1:185021600-185057200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:185024200-185044000	Weak transcription	Fetal Stomach	stomach
13	chr1:185024200-185056600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:185027200-185056400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:185027200-185056400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:185028200-185058200	Weak transcription	Brain Substantia Nigra	brain
17	chr1:185028800-185043400	Weak transcription	Small Intestine	intestine
18	chr1:185029600-185042600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:185030200-185041200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:185030200-185076600	Weak transcription	Gastric	stomach
21	chr1:185031200-185044000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:185031200-185044400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:185032200-185057800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr1:185032400-185041000	Weak transcription	Liver	Liver
25	chr1:185032400-185042400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:185032400-185044000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:185032800-185056600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:185033000-185040400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:185033200-185040400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr1:185033200-185044000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:185034200-185043400	Weak transcription	A549	lung
32	chr1:185034400-185044000	Weak transcription	Fetal Intestine Small	intestine
33	chr1:185034800-185044600	Weak transcription	Lung	lung
34	chr1:185034800-185057400	Weak transcription	Fetal Brain Female	brain
35	chr1:185034800-185077000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:185035000-185040400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:185035000-185044600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:185035000-185056600	Weak transcription	Fetal Muscle Leg	muscle
39	chr1:185035000-185058000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:185035200-185056600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:185035400-185040200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr1:185035400-185043000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:185035400-185057000	Weak transcription	Fetal Intestine Large	intestine
44	chr1:185035600-185040400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:185035800-185052600	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr1:185035800-185056400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:185035800-185057800	Weak transcription	Fetal Lung	lung
48	chr1:185036000-185040400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:185036000-185056600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:185036000-185056600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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