Variant report

Variant	rs399061
Chromosome Location	chr2:40438489-40438490
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs105288	0.88[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs1641452	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1641458	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1651356	0.83[ASN][1000 genomes]
rs36162999	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs366578	1.00[JPT][hapmap]
rs368642	0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs369140	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs371909	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs372052	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs373606	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs374159	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs374711	0.80[ASN][1000 genomes]
rs3749056	1.00[JPT][hapmap]
rs375180	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs376491	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs379410	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs379859	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs380082	0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[YRI][hapmap]
rs380975	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs383073	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs384511	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs384994	1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs385561	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs389109	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs389992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs391631	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs391984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs393711	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs394112	0.86[GIH][hapmap];1.00[JPT][hapmap]
rs394540	1.00[JPT][hapmap]
rs401815	1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs402307	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]
rs405884	1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs406222	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs406736	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs406880	1.00[JPT][hapmap]
rs407267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs407388	0.86[GIH][hapmap];1.00[JPT][hapmap]
rs407889	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs408009	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs408662	0.80[ASN][1000 genomes]
rs410031	0.83[ASN][1000 genomes]
rs410480	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs413711	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs414766	0.83[ASN][1000 genomes]
rs415695	0.88[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs417464	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];0.93[ASN][1000 genomes]
rs417591	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs417873	0.88[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs418780	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs421870	1.00[JPT][hapmap]
rs422411	0.84[ASN][1000 genomes]
rs423075	0.80[ASN][1000 genomes]
rs426295	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs427632	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs428738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs429227	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs430314	0.88[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.84[ASN][1000 genomes]
rs430394	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs430473	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs432142	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs432769	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs432981	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs434082	1.00[JPT][hapmap]
rs436010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs439960	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs440155	1.00[JPT][hapmap]
rs441196	0.85[CEU][hapmap];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	0.82[ASN][1000 genomes]
rs442476	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs442586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs443236	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs444504	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs450116	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs450823	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs451074	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs451158	1.00[JPT][hapmap]
rs451811	1.00[JPT][hapmap]
rs452138	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs479909	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4952596	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs505473	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs581477	0.88[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs581568	0.88[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs588179	0.84[ASN][1000 genomes]
rs615449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs666362	1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs678107	0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs679339	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs688673	0.88[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]

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	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
11	nsv526074	chr2:40423454-40451724	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40418200-40447200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr2:40418600-40445800	Weak transcription	Dnd41	blood
3	chr2:40430600-40439600	Weak transcription	HSMM	muscle
4	chr2:40430800-40439800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr2:40431200-40440600	Weak transcription	Fetal Stomach	stomach
6	chr2:40431400-40439800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:40431400-40440200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:40431800-40440000	Weak transcription	NHDF-Ad	bronchial
9	chr2:40432200-40440200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:40435600-40440000	Weak transcription	HSMMtube	muscle
11	chr2:40436000-40439600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:40436800-40440200	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:40437000-40438800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr2:40437000-40439000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr2:40437000-40439000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr2:40437000-40440400	Weak transcription	Left Ventricle	heart
17	chr2:40437200-40438600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:40437200-40440000	Enhancers	Fetal Heart	heart
19	chr2:40437200-40441600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:40437200-40453200	Weak transcription	Right Ventricle	heart
21	chr2:40438000-40447200	Weak transcription	Fetal Brain Male	brain
22	chr2:40438200-40438800	Enhancers	H9 Cell Line	embryonic stem cell
23	chr2:40438200-40438800	Enhancers	Osteobl	bone
24	chr2:40438200-40439000	Enhancers	HUES48 Cell Line	embryonic stem cell

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