Variant report

Variant	rs402307
Chromosome Location	chr2:40454945-40454946
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs105288	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1641452	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1641456	0.83[ASN][1000 genomes]
rs1641457	0.83[ASN][1000 genomes]
rs1641458	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1651355	0.83[ASN][1000 genomes]
rs1651356	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34971853	0.83[ASN][1000 genomes]
rs36162999	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36184451	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs366578	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs368642	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs369140	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs371909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs372052	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs373606	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs374159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374711	0.84[ASN][1000 genomes]
rs3749056	1.00[JPT][hapmap]
rs375180	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs376170	0.83[ASN][1000 genomes]
rs376491	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs379410	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs379859	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs380082	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs380975	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs383073	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs384511	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs384791	0.83[ASN][1000 genomes]
rs384994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385561	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs389109	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs389992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs391631	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs391984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs393711	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs394112	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs394540	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs399061	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs401815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs405884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs406222	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs406736	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs406880	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs407267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407388	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs407889	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs408009	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs408662	0.84[ASN][1000 genomes]
rs410480	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs413711	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs415695	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs417464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs417591	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs417873	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs418380	0.83[ASN][1000 genomes]
rs418780	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs421870	1.00[JPT][hapmap]
rs422411	0.81[ASN][1000 genomes]
rs423075	0.84[ASN][1000 genomes]
rs426295	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs427632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs428738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs429227	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs430314	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs430394	0.97[ASN][1000 genomes]
rs430473	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs432142	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs432769	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs432981	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434082	1.00[JPT][hapmap]
rs434326	0.83[ASN][1000 genomes]
rs436010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs439960	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs440155	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs441196	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs441413	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs441593	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs441802	0.85[ASN][1000 genomes]
rs442476	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs443236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs444504	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs450116	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs450823	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs451074	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs451158	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs451811	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs452138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479909	0.97[ASN][1000 genomes]
rs4952596	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs505473	1.00[JPT][hapmap]
rs581477	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs581568	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs588179	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs615449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs666362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs678107	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs679339	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs688673	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs72794789	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
4	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
5	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
6	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
7	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
8	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
9	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1008190	chr2:40429442-40506772	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv34071	chr2:40435231-40578229	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv524586	chr2:40447587-40497501	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40446400-40455400	Weak transcription	Psoas Muscle	Psoas
2	chr2:40447800-40457600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:40448000-40487400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr2:40448200-40455400	Weak transcription	HSMM	muscle
5	chr2:40451400-40455600	Weak transcription	Aorta	Aorta
6	chr2:40451400-40490000	Weak transcription	Dnd41	blood
7	chr2:40452600-40455600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr2:40453600-40455400	Weak transcription	Left Ventricle	heart
9	chr2:40453600-40455400	Weak transcription	HSMMtube	muscle
10	chr2:40453600-40455600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr2:40453600-40455800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:40453600-40457200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:40453600-40457200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:40453600-40459400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:40453800-40455600	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:40453800-40455600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:40453800-40471000	Weak transcription	Right Ventricle	heart
18	chr2:40453800-40471400	Weak transcription	Right Atrium	heart
19	chr2:40454000-40455000	Weak transcription	Brain Germinal Matrix	brain
20	chr2:40454000-40455600	Weak transcription	Fetal Brain Male	brain
21	chr2:40454200-40455400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:40454200-40458000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:40454400-40458200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:40454600-40455000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:40454600-40457400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:40454600-40459200	Enhancers	Fetal Heart	heart

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