Variant report

Variant	rs6878733
Chromosome Location	chr5:114556193-114556194
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10045548	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10059069	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10076833	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10079380	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11745083	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes]
rs11745170	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs11960213	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17640052	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2303001	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs265406	0.87[JPT][hapmap]
rs265409	0.87[JPT][hapmap]
rs265413	0.87[JPT][hapmap]
rs267297	0.82[CEU][hapmap]
rs267298	0.82[CEU][hapmap]
rs3805580	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs3805581	0.89[EUR][1000 genomes]
rs3805586	0.90[GIH][hapmap];0.81[AMR][1000 genomes]
rs62383165	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6594883	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs67276221	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6884828	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6886102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7706217	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7725831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9326954	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830454	chr5:114453864-114607159	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1029371	chr5:114541428-114590891	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6878733	CCDC112	cis	parietal	SCAN
rs6878733	PGGT1B	cis	multi-tissue	Pritchard
rs6878733	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs6878733	PGGT1B	cis	normal skin	skin_eQTL
rs6878733	PGGT1B	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114523400-114576200	Weak transcription	Psoas Muscle	Psoas
2	chr5:114528000-114563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:114529200-114562600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:114530200-114562600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:114530200-114562600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr5:114530600-114594400	Weak transcription	Pancreas	Pancrea
7	chr5:114530800-114565200	Weak transcription	NHDF-Ad	bronchial
8	chr5:114531000-114558800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:114538400-114567000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:114538400-114572000	Weak transcription	Lung	lung
11	chr5:114539200-114580200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:114539800-114566000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:114540800-114567600	Weak transcription	Hela-S3	cervix
14	chr5:114541000-114562000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr5:114541800-114573400	Weak transcription	NHLF	lung
16	chr5:114542000-114575800	Weak transcription	Small Intestine	intestine
17	chr5:114543600-114558800	Weak transcription	NH-A	brain
18	chr5:114543600-114562400	Weak transcription	HUVEC	blood vessel
19	chr5:114543800-114562800	Weak transcription	Colon Smooth Muscle	Colon
20	chr5:114543800-114565400	Weak transcription	Brain Hippocampus Middle	brain
21	chr5:114543800-114577800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:114545400-114562400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:114545400-114563200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:114546000-114562600	Weak transcription	GM12878-XiMat	blood
25	chr5:114546000-114563000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:114546600-114556600	Weak transcription	HepG2	liver
27	chr5:114546600-114560800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr5:114546800-114575600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr5:114546800-114578000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr5:114547600-114563800	Weak transcription	Thymus	Thymus
31	chr5:114547600-114577600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr5:114547800-114559000	Weak transcription	Spleen	Spleen
33	chr5:114547800-114578400	Weak transcription	Esophagus	oesophagus
34	chr5:114547800-114596600	Weak transcription	Brain Germinal Matrix	brain
35	chr5:114548400-114596800	Weak transcription	K562	blood
36	chr5:114548600-114562400	Weak transcription	Fetal Kidney	kidney
37	chr5:114548600-114563000	Weak transcription	Colonic Mucosa	Colon
38	chr5:114548800-114575400	Weak transcription	Brain Substantia Nigra	brain
39	chr5:114549400-114562800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr5:114549400-114597200	Weak transcription	Aorta	Aorta
41	chr5:114549600-114562000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:114549600-114562800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr5:114549600-114563000	Weak transcription	Ovary	ovary
44	chr5:114549600-114564600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr5:114549600-114565400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr5:114549600-114565600	Weak transcription	Osteobl	bone
47	chr5:114549600-114574400	Weak transcription	HMEC	breast
48	chr5:114549800-114557200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr5:114549800-114559000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:114549800-114562800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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