Variant report

Variant	rs401815
Chromosome Location	chr2:40467170-40467171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs105288	0.88[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs1641452	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1641458	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1651356	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34971853	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36162999	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36184451	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs366578	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap];0.88[EUR][1000 genomes]
rs368642	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs369140	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs371909	1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs372052	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs373606	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs374159	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3749056	1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs375180	0.82[AMR][1000 genomes]
rs376491	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs378702	0.80[AMR][1000 genomes]
rs379410	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap]
rs379859	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs380082	0.85[ASW][hapmap];0.82[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs380975	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs383073	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384511	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs384994	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs385561	0.84[ASW][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs389109	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs389992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs391631	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs391984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs393711	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs394112	0.85[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs394540	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs398175	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs399061	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[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];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs406222	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs406736	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[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];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs407388	0.85[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs407889	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs408009	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs410480	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs413711	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs415695	0.82[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs417464	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];0.94[ASN][1000 genomes]
rs417591	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs417873	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs418780	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs421870	1.00[JPT][hapmap]
rs426295	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs427632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs428738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs429227	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs430314	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs430394	0.88[ASN][1000 genomes]
rs430473	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs432142	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs432769	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs432981	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs434082	1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs436010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs439960	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs440155	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][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]
rs442476	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs442586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs443236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs444504	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs450116	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs450823	0.82[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];1.00[ASN][1000 genomes]
rs451074	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs451158	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs451811	0.82[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs452138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs479909	0.88[ASN][1000 genomes]
rs4952596	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505473	0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs581477	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs581568	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs588179	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs615449	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs666362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674128	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs678107	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs679339	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs688673	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs72794789	0.93[EUR][1000 genomes];0.91[ASN][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	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	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
3	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
4	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
5	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
6	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:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40448000-40487400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr2:40451400-40490000	Weak transcription	Dnd41	blood
3	chr2:40453800-40471000	Weak transcription	Right Ventricle	heart
4	chr2:40453800-40471400	Weak transcription	Right Atrium	heart
5	chr2:40458600-40467200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:40465600-40468000	Enhancers	Rectal Smooth Muscle	rectum
7	chr2:40465800-40468800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:40465800-40469600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:40466000-40468200	Enhancers	Colon Smooth Muscle	Colon
10	chr2:40466200-40467200	Weak transcription	Pancreas	Pancrea
11	chr2:40466200-40468600	Enhancers	Fetal Heart	heart
12	chr2:40466400-40468200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:40466600-40468000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:40466600-40468000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:40466600-40468000	Enhancers	Fetal Muscle Leg	muscle
16	chr2:40466600-40468000	Enhancers	Fetal Stomach	stomach
17	chr2:40466600-40468000	Enhancers	NHLF	lung
18	chr2:40466600-40468200	Enhancers	Adipose Nuclei	Adipose
19	chr2:40466600-40468200	Enhancers	Osteobl	bone
20	chr2:40466600-40468600	Enhancers	NHDF-Ad	bronchial
21	chr2:40466800-40467200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:40466800-40467200	Enhancers	Brain Anterior Caudate	brain
23	chr2:40466800-40467400	Weak transcription	Left Ventricle	heart
24	chr2:40466800-40468000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr2:40466800-40468000	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr2:40466800-40468000	Enhancers	Fetal Lung	lung
27	chr2:40466800-40468000	Enhancers	HSMM	muscle
28	chr2:40467000-40467400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr2:40467000-40467600	Enhancers	Brain Germinal Matrix	brain
30	chr2:40467000-40467600	Active TSS	Brain Substantia Nigra	brain
31	chr2:40467000-40467600	Enhancers	Psoas Muscle	Psoas
32	chr2:40467000-40467600	Active TSS	Stomach Smooth Muscle	stomach
33	chr2:40467000-40468000	Enhancers	HMEC	breast
34	chr2:40467000-40468000	Enhancers	HSMMtube	muscle
35	chr2:40467000-40468000	Enhancers	NH-A	brain

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