Variant report

Variant	rs407388
Chromosome Location	chr2:40473868-40473869
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:40472223..40475000-chr2:40477866..40479502,2	K562	blood:

Variant related genes	Relation type
ENSG00000227028	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs105288	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs1641452	0.88[EUR][1000 genomes]
rs1641458	1.00[JPT][hapmap]
rs1651356	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34971853	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36162999	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36184451	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs366578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs368642	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs369140	1.00[JPT][hapmap]
rs371909	0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs372052	1.00[JPT][hapmap]
rs373606	0.90[JPT][hapmap]
rs374159	0.82[EUR][1000 genomes]
rs3749056	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.93[ASN][1000 genomes]
rs379410	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap]
rs379859	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs380082	1.00[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs380975	1.00[JPT][hapmap]
rs383073	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs384511	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs384994	0.85[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap]
rs385561	1.00[JPT][hapmap]
rs389109	1.00[JPT][hapmap]
rs389992	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs391631	1.00[JPT][hapmap]
rs391984	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs393711	1.00[JPT][hapmap]
rs394112	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs394540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs398175	0.88[EUR][1000 genomes]
rs399061	0.86[GIH][hapmap];1.00[JPT][hapmap]
rs401815	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]
rs402307	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs405884	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs406222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs406736	0.84[EUR][1000 genomes]
rs406880	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs407267	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs407889	1.00[JPT][hapmap]
rs408009	1.00[JPT][hapmap]
rs410480	0.82[EUR][1000 genomes]
rs413711	1.00[JPT][hapmap]
rs415695	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs417464	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs417591	1.00[JPT][hapmap]
rs417873	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs418780	0.90[JPT][hapmap]
rs421870	1.00[JPT][hapmap]
rs426295	1.00[JPT][hapmap]
rs427632	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[EUR][1000 genomes]
rs428738	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs429227	0.82[EUR][1000 genomes]
rs430314	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs430473	0.82[EUR][1000 genomes]
rs432142	0.88[EUR][1000 genomes]
rs432769	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs434082	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.95[ASN][1000 genomes]
rs436010	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs439960	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs440155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs441196	1.00[JPT][hapmap]
rs441413	0.90[JPT][hapmap]
rs441593	1.00[JPT][hapmap]
rs442586	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs443236	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs450116	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs450823	0.82[CEU][hapmap];1.00[JPT][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]
rs451074	0.81[JPT][hapmap]
rs451158	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs451811	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452138	0.85[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[YRI][hapmap]
rs4952596	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs505473	1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs581477	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs581568	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs588179	0.82[ASN][1000 genomes]
rs615449	0.83[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs666362	1.00[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs674128	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs679339	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs688673	1.00[JPT][hapmap]
rs72794789	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv873912	chr2:40468418-40492315	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv873913	chr2:40469705-40485074	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 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	chr2:40467800-40487400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:40468000-40476600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:40469000-40475200	Enhancers	Fetal Heart	heart
6	chr2:40469800-40474400	Enhancers	Rectal Smooth Muscle	rectum
7	chr2:40470400-40481200	Weak transcription	Brain Germinal Matrix	brain
8	chr2:40470800-40474800	Enhancers	Fetal Intestine Small	intestine
9	chr2:40471200-40474600	Enhancers	Fetal Intestine Large	intestine
10	chr2:40471200-40474600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:40472200-40474400	Weak transcription	Fetal Lung	lung
12	chr2:40472200-40478600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:40472400-40475800	Weak transcription	Hela-S3	cervix
14	chr2:40472400-40478400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:40472600-40475400	Weak transcription	Right Atrium	heart
16	chr2:40472600-40477800	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:40472600-40487200	Weak transcription	HSMM	muscle
18	chr2:40472800-40474200	Weak transcription	Osteobl	bone
19	chr2:40472800-40478400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:40473400-40474000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr2:40473400-40474600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:40473400-40474600	Enhancers	Fetal Stomach	stomach
23	chr2:40473600-40474000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:40473600-40474000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr2:40473600-40474800	Enhancers	Left Ventricle	heart
26	chr2:40473800-40474200	Weak transcription	Right Ventricle	heart
27	chr2:40473800-40474200	Weak transcription	Stomach Smooth Muscle	stomach

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