Variant report

Variant	rs1641458
Chromosome Location	chr2:40421694-40421695
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	chr2:40419927..40421772-chr2:40425195..40428157,2	MCF-7	breast:

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs105288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs118899	0.89[ASN][1000 genomes]
rs1641452	0.83[ASN][1000 genomes]
rs1641456	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1641457	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1651355	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28628343	0.89[ASN][1000 genomes]
rs35487690	0.83[ASN][1000 genomes]
rs366578	1.00[JPT][hapmap]
rs368642	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs369140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371909	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs372052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373602	0.95[ASN][1000 genomes]
rs373606	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs374159	0.83[ASN][1000 genomes]
rs374711	0.99[ASN][1000 genomes]
rs3749056	1.00[JPT][hapmap]
rs375180	0.99[ASN][1000 genomes]
rs376170	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376491	0.89[ASN][1000 genomes]
rs379410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs380082	1.00[JPT][hapmap]
rs380975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs384791	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384994	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs385561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389992	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs391631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs391984	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs393711	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394112	1.00[JPT][hapmap]
rs394540	1.00[JPT][hapmap]
rs399061	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs401815	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs402307	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs405884	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs406222	1.00[JPT][hapmap]
rs406736	0.83[ASN][1000 genomes]
rs406880	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs407267	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs407388	1.00[JPT][hapmap]
rs407889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs408009	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs408662	0.96[ASN][1000 genomes]
rs410031	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs410480	0.96[ASN][1000 genomes]
rs413711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs414766	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs415695	1.00[JPT][hapmap]
rs417464	0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs417591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs417873	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs418380	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418780	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs421870	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs422411	0.95[ASN][1000 genomes]
rs423075	0.99[ASN][1000 genomes]
rs426295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427632	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs428738	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs429227	0.83[ASN][1000 genomes]
rs430314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs430394	0.80[ASN][1000 genomes]
rs430473	0.95[ASN][1000 genomes]
rs432769	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs432981	0.83[ASN][1000 genomes]
rs434082	1.00[JPT][hapmap]
rs434326	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436010	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs439960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs440155	1.00[JPT][hapmap]
rs441196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs441413	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs441593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs441802	0.97[ASN][1000 genomes]
rs442476	0.83[ASN][1000 genomes]
rs442586	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs443236	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs450116	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs450823	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs451074	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs451158	1.00[JPT][hapmap]
rs451811	1.00[JPT][hapmap]
rs452138	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs479909	0.80[ASN][1000 genomes]
rs505473	1.00[JPT][hapmap]
rs581477	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs581568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs615449	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs666362	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs678107	1.00[JPT][hapmap]
rs679339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs688673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv873910	chr2:40391907-40466268	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv2763455	chr2:40416373-40433420	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1001866	chr2:40416373-40433420	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv581503	chr2:40417012-40430611	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv581504	chr2:40418386-40430611	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv526425	chr2:40418386-40447587	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	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	chr2:40400600-40426800	Weak transcription	Osteobl	bone
2	chr2:40405400-40430000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:40405600-40421800	Weak transcription	Right Ventricle	heart
4	chr2:40411000-40424200	Weak transcription	HSMMtube	muscle
5	chr2:40412000-40421800	Weak transcription	Left Ventricle	heart
6	chr2:40416000-40425800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:40417200-40430400	Weak transcription	Aorta	Aorta
8	chr2:40417800-40424200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:40417800-40424400	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:40418200-40447200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr2:40418600-40445800	Weak transcription	Dnd41	blood
12	chr2:40419200-40436600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:40420000-40422200	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr2:40420000-40422600	Enhancers	Stomach Mucosa	stomach
15	chr2:40420000-40422800	Enhancers	Fetal Intestine Large	intestine
16	chr2:40420400-40422600	Enhancers	Fetal Intestine Small	intestine
17	chr2:40420400-40423600	Weak transcription	HSMM	muscle
18	chr2:40420400-40426200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:40420600-40421800	Weak transcription	Gastric	stomach
20	chr2:40420600-40421800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:40420600-40422200	Enhancers	Fetal Heart	heart
22	chr2:40420600-40424800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:40420600-40430000	Weak transcription	NHLF	lung
24	chr2:40420800-40428800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:40421000-40421800	Weak transcription	Fetal Kidney	kidney
26	chr2:40421000-40422000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:40421000-40423800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:40421000-40424400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:40421200-40429200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:40421600-40421800	Enhancers	Fetal Brain Male	brain
31	chr2:40421600-40422400	Enhancers	Rectal Mucosa Donor 31	rectum

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