Variant report

Variant	rs73040411
Chromosome Location	chr2:189262591-189262592
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189156172..189158874-chr2:189261815..189263750,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144366	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10168173	1.00[EUR][1000 genomes]
rs10497688	1.00[EUR][1000 genomes]
rs11678294	0.92[AFR][1000 genomes]
rs11683340	0.92[AFR][1000 genomes]
rs13393870	1.00[EUR][1000 genomes]
rs13394334	1.00[EUR][1000 genomes]
rs13430185	1.00[EUR][1000 genomes]
rs13430412	1.00[EUR][1000 genomes]
rs16829866	1.00[EUR][1000 genomes]
rs16829915	1.00[EUR][1000 genomes]
rs16829922	1.00[EUR][1000 genomes]
rs58715158	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58718952	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59058494	1.00[EUR][1000 genomes]
rs59329932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60885306	1.00[EUR][1000 genomes]
rs61163899	1.00[EUR][1000 genomes]
rs6705443	1.00[EUR][1000 genomes]
rs6709650	1.00[EUR][1000 genomes]
rs6716922	1.00[EUR][1000 genomes]
rs6721812	1.00[EUR][1000 genomes]
rs73036471	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73036479	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73036496	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73040428	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73040439	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73040441	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73040442	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73040450	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73040454	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73041610	1.00[EUR][1000 genomes]
rs73041636	1.00[EUR][1000 genomes]
rs73041644	1.00[EUR][1000 genomes]
rs73041648	1.00[EUR][1000 genomes]
rs73041649	1.00[EUR][1000 genomes]
rs7340152	1.00[EUR][1000 genomes]
rs7560857	1.00[EUR][1000 genomes]
rs7577096	1.00[EUR][1000 genomes]
rs7577467	1.00[EUR][1000 genomes]
rs7586703	1.00[EUR][1000 genomes]
rs7588114	1.00[EUR][1000 genomes]
rs7592433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7592539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7596417	1.00[EUR][1000 genomes]
rs7597930	1.00[EUR][1000 genomes]
rs7598380	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7599101	1.00[EUR][1000 genomes]
rs9653310	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010394	chr2:188994398-189284092	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv998395	chr2:189018246-189284092	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1010330	chr2:189182307-189265614	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv999135	chr2:189184937-189265614	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv534341	chr2:189200405-189368467	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv533786	chr2:189248503-189354495	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189251000-189285200	Weak transcription	Aorta	Aorta
2	chr2:189251200-189268400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:189251200-189269000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:189251200-189269400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:189251200-189269400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:189251200-189270000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:189251200-189270200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:189251800-189263600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:189254800-189267200	Weak transcription	Ovary	ovary
10	chr2:189256000-189270600	Weak transcription	Fetal Lung	lung
11	chr2:189256400-189269000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:189258600-189263600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:189258800-189263400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:189259800-189262600	Enhancers	Gastric	stomach
15	chr2:189261200-189263400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:189261200-189268400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:189261400-189263600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:189261400-189269200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:189261400-189269400	Weak transcription	Placenta	Placenta
20	chr2:189261600-189268400	Weak transcription	Fetal Intestine Small	intestine
21	chr2:189261600-189270000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:189261800-189264000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:189261800-189269200	Weak transcription	Fetal Stomach	stomach
24	chr2:189261800-189269800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:189262200-189262800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
26	chr2:189262200-189263000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:189262400-189262800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:189262400-189262800	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr2:189262400-189263000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr2:189262400-189263000	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr2:189262400-189263000	Strong transcription	HUES6 Cell Line	embryonic stem cell

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