Variant report

Variant	rs426899
Chromosome Location	chr5:118831035-118831036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118827883..118830357-chr5:118830645..118832803,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133835	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs2257900	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2257901	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455463	0.87[ASN][1000 genomes]
rs2459726	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs246965	0.80[AMR][1000 genomes]
rs2546210	0.81[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs257970	0.89[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs257976	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs257978	0.90[ASN][1000 genomes]
rs26181	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs26184	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2636961	0.84[CEU][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2636962	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2636964	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2636968	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2678070	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[ASN][1000 genomes]
rs2678074	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2678076	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2678091	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs27938	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs32640	0.84[ASN][1000 genomes]
rs32651	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs32664	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs382719	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs389760	0.82[ASN][1000 genomes]
rs39970	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422297	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs439954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs442923	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs450118	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs460274	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs461108	0.91[MEX][hapmap]
rs463098	0.89[CEU][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs463513	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs465091	0.85[CEU][hapmap]
rs467076	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6875595	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs7721602	0.85[CEU][hapmap];0.91[MEX][hapmap]

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	nsv1030717	chr5:118709310-118836951	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs426899	PRR16	cis	parietal	SCAN
rs426899	SNX24	cis	parietal	SCAN
rs426899	HSD17B4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118789400-118831200	Weak transcription	NH-A	brain
2	chr5:118789400-118831600	Weak transcription	HSMMtube	muscle
3	chr5:118791800-118846600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:118794800-118861200	Weak transcription	HSMM	muscle
5	chr5:118804200-118879600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr5:118804800-118837000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:118805200-118839400	Weak transcription	NHEK	skin
8	chr5:118806000-118846400	Weak transcription	Esophagus	oesophagus
9	chr5:118806000-118846400	Weak transcription	Spleen	Spleen
10	chr5:118806200-118831400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:118806200-118844800	Weak transcription	Thymus	Thymus
12	chr5:118806200-118846400	Weak transcription	Pancreas	Pancrea
13	chr5:118806200-118855600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:118806400-118831200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:118806400-118845000	Weak transcription	Fetal Stomach	stomach
16	chr5:118806400-118846400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:118806600-118832000	Weak transcription	HUVEC	blood vessel
18	chr5:118806800-118845400	Weak transcription	Fetal Heart	heart
19	chr5:118808000-118839600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr5:118808000-118839800	Weak transcription	Psoas Muscle	Psoas
21	chr5:118809600-118838000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr5:118811200-118839600	Weak transcription	Brain Germinal Matrix	brain
23	chr5:118812000-118846400	Weak transcription	NHLF	lung
24	chr5:118812200-118833800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:118814000-118831200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:118814000-118831200	Weak transcription	Small Intestine	intestine
27	chr5:118814000-118838200	Weak transcription	Fetal Intestine Small	intestine
28	chr5:118814000-118845000	Weak transcription	Gastric	stomach
29	chr5:118814000-118845200	Weak transcription	Aorta	Aorta
30	chr5:118814200-118831600	Weak transcription	A549	lung
31	chr5:118814600-118831800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr5:118814600-118832600	Weak transcription	Colonic Mucosa	Colon
33	chr5:118814800-118832200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:118814800-118839400	Weak transcription	Right Ventricle	heart
35	chr5:118814800-118844800	Weak transcription	Lung	lung
36	chr5:118815000-118831800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:118815400-118831400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr5:118815400-118835400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr5:118815400-118839000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:118815600-118831600	Weak transcription	Fetal Muscle Leg	muscle
41	chr5:118815800-118831400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr5:118815800-118831400	Weak transcription	Ovary	ovary
43	chr5:118815800-118831800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr5:118815800-118839000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr5:118815800-118845400	Weak transcription	HMEC	breast
46	chr5:118816000-118844000	Weak transcription	Hela-S3	cervix
47	chr5:118816000-118847000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr5:118816800-118834200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:118816800-118837800	Strong transcription	Dnd41	blood
50	chr5:118816800-118839600	Strong transcription	Adipose Nuclei	Adipose

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