Variant report

Variant	rs455949
Chromosome Location	chr5:118837833-118837834
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10051019	0.81[JPT][hapmap]
rs10078097	0.82[JPT][hapmap]
rs10478426	0.82[JPT][hapmap]
rs11241506	0.80[JPT][hapmap]
rs12658566	0.82[JPT][hapmap]
rs13361193	0.82[JPT][hapmap]
rs161855	0.83[ASN][1000 genomes]
rs2075698	0.82[JPT][hapmap]
rs2259347	0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2287712	0.86[JPT][hapmap]
rs2303003	0.82[JPT][hapmap]
rs2451816	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2546210	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs25640	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs257970	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs257972	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs257973	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs257974	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs26180	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2678070	0.89[CEU][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap]
rs2945327	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs32659	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs32662	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs32665	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap]
rs3756512	0.82[JPT][hapmap]
rs3797363	0.82[JPT][hapmap]
rs3797364	0.82[JPT][hapmap]
rs3822525	0.82[JPT][hapmap]
rs3850200	0.86[JPT][hapmap]
rs457106	0.82[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs461108	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs463098	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs463513	0.89[CEU][hapmap]
rs465091	0.86[CHB][hapmap]
rs4895372	0.86[CHB][hapmap]
rs6875595	0.82[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap]
rs6894991	0.82[JPT][hapmap]
rs6895345	0.82[JPT][hapmap]
rs7721602	0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1016271	chr5:118836891-119487982	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2486573	chr5:118837315-118838827	Weak transcription Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs455949	PRR16	cis	parietal	SCAN
rs455949	HSD17B4	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118791800-118846600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:118794800-118861200	Weak transcription	HSMM	muscle
3	chr5:118804200-118879600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:118805200-118839400	Weak transcription	NHEK	skin
5	chr5:118806000-118846400	Weak transcription	Esophagus	oesophagus
6	chr5:118806000-118846400	Weak transcription	Spleen	Spleen
7	chr5:118806200-118844800	Weak transcription	Thymus	Thymus
8	chr5:118806200-118846400	Weak transcription	Pancreas	Pancrea
9	chr5:118806200-118855600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:118806400-118845000	Weak transcription	Fetal Stomach	stomach
11	chr5:118806400-118846400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:118806800-118845400	Weak transcription	Fetal Heart	heart
13	chr5:118808000-118839600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr5:118808000-118839800	Weak transcription	Psoas Muscle	Psoas
15	chr5:118809600-118838000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:118811200-118839600	Weak transcription	Brain Germinal Matrix	brain
17	chr5:118812000-118846400	Weak transcription	NHLF	lung
18	chr5:118814000-118838200	Weak transcription	Fetal Intestine Small	intestine
19	chr5:118814000-118845000	Weak transcription	Gastric	stomach
20	chr5:118814000-118845200	Weak transcription	Aorta	Aorta
21	chr5:118814800-118839400	Weak transcription	Right Ventricle	heart
22	chr5:118814800-118844800	Weak transcription	Lung	lung
23	chr5:118815400-118839000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:118815800-118839000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr5:118815800-118845400	Weak transcription	HMEC	breast
26	chr5:118816000-118844000	Weak transcription	Hela-S3	cervix
27	chr5:118816000-118847000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr5:118816800-118839600	Strong transcription	Adipose Nuclei	Adipose
29	chr5:118817000-118846400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr5:118817200-118839600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:118818400-118839600	Weak transcription	Fetal Kidney	kidney
32	chr5:118819000-118839200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr5:118819600-118844400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr5:118820000-118839000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr5:118820000-118839600	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr5:118820200-118838600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr5:118820200-118846400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr5:118820400-118838800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr5:118821000-118839600	Strong transcription	Liver	Liver
40	chr5:118821000-118843800	Weak transcription	NHDF-Ad	bronchial
41	chr5:118824200-118838400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:118827600-118847800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr5:118828000-118840400	Weak transcription	Osteobl	bone
44	chr5:118829200-118840200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr5:118829600-118839600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr5:118829800-118844800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr5:118830400-118845200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:118831000-118838000	Strong transcription	Primary B cells from cord blood	blood
49	chr5:118831000-118840200	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr5:118831800-118838000	Strong transcription	Rectal Mucosa Donor 31	rectum

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