Variant report

Variant	rs42679
Chromosome Location	chr5:14810068-14810069
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14809897..14811757-chr5:14812423..14814739,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1061813	0.89[CEU][hapmap];0.93[CHB][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11133799	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1117282	0.83[ASN][1000 genomes]
rs12653321	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13155894	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1353258	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1812658	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2453316	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs258218	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs258219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs258222	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258224	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258226	1.00[CEU][hapmap];0.93[CHB][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258227	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258228	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258231	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs25957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28005	0.96[ASN][1000 genomes]
rs28006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28108	0.98[ASN][1000 genomes]
rs30615	0.89[ASN][1000 genomes]
rs31909	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs31912	0.96[CEU][hapmap];0.93[CHB][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs31933	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs31990	0.96[CEU][hapmap];0.87[CHB][hapmap]
rs33102	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs39636	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs39916	0.93[ASN][1000 genomes]
rs42680	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs573116	0.87[ASN][1000 genomes]
rs826352	0.88[CEU][hapmap];0.93[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs826357	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs879253	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9790982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv948447	chr5:14771247-14852610	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830212	chr5:14784197-14966683	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14777200-14810400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr5:14777200-14811400	Weak transcription	Colonic Mucosa	Colon
3	chr5:14778200-14817200	Weak transcription	Fetal Brain Female	brain
4	chr5:14796400-14821800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr5:14801200-14811200	Weak transcription	Esophagus	oesophagus
6	chr5:14806800-14811000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:14807000-14810800	Weak transcription	Fetal Heart	heart
8	chr5:14809400-14810800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:14809400-14811200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:14809400-14811600	Enhancers	HMEC	breast
11	chr5:14809400-14812800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr5:14809400-14813400	Enhancers	Primary B cells from peripheral blood	blood
13	chr5:14809600-14810200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr5:14809600-14810200	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr5:14809600-14810200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:14809600-14810200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:14809600-14810200	Enhancers	Lung	lung
18	chr5:14809600-14810200	Enhancers	Placenta Amnion	Placenta Amnion
19	chr5:14809600-14810200	Enhancers	Spleen	Spleen
20	chr5:14809600-14810200	Enhancers	HSMMtube	muscle
21	chr5:14809600-14810400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr5:14809600-14810400	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr5:14809600-14810400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:14809600-14810400	Flanking Active TSS	Brain Cingulate Gyrus	brain
25	chr5:14809600-14810400	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr5:14809600-14810400	Enhancers	K562	blood
27	chr5:14809600-14810600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:14809600-14810600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr5:14809600-14810600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr5:14809600-14810600	Flanking Active TSS	Hela-S3	cervix
31	chr5:14809600-14810800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr5:14809600-14810800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr5:14809600-14811000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr5:14809600-14811000	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr5:14809600-14811000	Enhancers	Brain Substantia Nigra	brain
36	chr5:14809600-14811400	Strong transcription	Fetal Intestine Small	intestine
37	chr5:14809600-14811400	Enhancers	Small Intestine	intestine
38	chr5:14809600-14811400	Enhancers	HepG2	liver
39	chr5:14809600-14811400	Enhancers	HSMM	muscle
40	chr5:14809600-14811400	Enhancers	NHLF	lung
41	chr5:14809600-14811600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:14809600-14811600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr5:14809600-14811600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr5:14809600-14811600	Enhancers	Primary hematopoietic stem cells	blood
45	chr5:14809600-14811600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr5:14809600-14811600	Enhancers	Liver	Liver
47	chr5:14809600-14811600	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr5:14809600-14811600	Enhancers	Psoas Muscle	Psoas
49	chr5:14809600-14811600	Enhancers	Right Ventricle	heart
50	chr5:14809600-14811600	Enhancers	HUVEC	blood vessel

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