Variant report

Variant	rs856049
Chromosome Location	chr1:158990412-158990413
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1057024	0.80[CHB][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];1.00[ASN][1000 genomes]
rs10908699	1.00[ASN][1000 genomes]
rs1101988	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1101993	0.86[EUR][1000 genomes]
rs1101994	0.86[EUR][1000 genomes]
rs1101995	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs1101996	0.86[EUR][1000 genomes]
rs1101997	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1101998	0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs11265131	0.86[CEU][hapmap];0.95[EUR][1000 genomes]
rs12059564	0.95[ASN][1000 genomes]
rs12087333	0.86[EUR][1000 genomes]
rs12120311	0.86[EUR][1000 genomes]
rs12139793	0.86[EUR][1000 genomes]
rs56248786	0.86[EUR][1000 genomes]
rs56348543	0.86[EUR][1000 genomes]
rs7525853	0.86[EUR][1000 genomes]
rs7535856	0.86[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs7540687	0.86[EUR][1000 genomes]
rs856043	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs856044	0.98[ASN][1000 genomes]
rs856046	0.82[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs856050	0.93[EUR][1000 genomes]
rs856054	0.94[CHB][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[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	esv3376764	chr1:158761947-158998617	Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3369957	chr1:158915589-159003393	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv872486	chr1:158979191-159090256	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs856049	CCDC19	cis	lymphoblastoid	seeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158976000-159000800	Weak transcription	Gastric	stomach
2	chr1:158980200-159025400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:158982600-159027400	Weak transcription	Fetal Kidney	kidney
4	chr1:158982800-159000200	Weak transcription	Aorta	Aorta
5	chr1:158984000-158991600	Strong transcription	Fetal Lung	lung
6	chr1:158984000-159000800	Weak transcription	Right Ventricle	heart
7	chr1:158984200-158991400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:158984200-159024200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:158984400-158995200	Strong transcription	Fetal Intestine Large	intestine
10	chr1:158984800-159027400	Weak transcription	Psoas Muscle	Psoas
11	chr1:158985400-159023800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:158985600-158991000	Strong transcription	Placenta	Placenta
13	chr1:158985600-158995200	Strong transcription	Thymus	Thymus
14	chr1:158985800-158991000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:158985800-158991600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:158985800-158991600	Strong transcription	Liver	Liver
17	chr1:158985800-158991600	Strong transcription	Duodenum Mucosa	Duodenum
18	chr1:158985800-158994400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:158985800-158995200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:158985800-159005000	Weak transcription	Brain Angular Gyrus	brain
21	chr1:158986000-158990800	Strong transcription	NHEK	skin
22	chr1:158986000-158991200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:158986000-158991600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr1:158986000-158991600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:158986000-158991800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:158986000-158992400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:158986000-158994000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:158986000-158995000	Strong transcription	HSMM	muscle
29	chr1:158986000-158995200	Strong transcription	Osteobl	bone
30	chr1:158986000-159016200	Weak transcription	Stomach Mucosa	stomach
31	chr1:158986200-158992600	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr1:158986800-158991600	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:158987000-158995000	Strong transcription	HUVEC	blood vessel
34	chr1:158987000-158995200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:158987000-159000200	Weak transcription	Brain Substantia Nigra	brain
36	chr1:158987000-159000400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:158987200-158991000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
38	chr1:158987200-158991200	Strong transcription	Fetal Muscle Leg	muscle
39	chr1:158987200-158991600	Strong transcription	Hela-S3	cervix
40	chr1:158987200-158991800	Strong transcription	Adipose Nuclei	Adipose
41	chr1:158987200-158992200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr1:158987200-158996200	Strong transcription	Primary hematopoietic stem cells	blood
43	chr1:158987200-158998400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:158987200-159000000	Weak transcription	Small Intestine	intestine
45	chr1:158987200-159000200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:158987200-159000400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:158987200-159001200	Strong transcription	Fetal Thymus	thymus
48	chr1:158987600-158996400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr1:158987800-158992000	Weak transcription	Fetal Stomach	stomach
50	chr1:158987800-158993400	Weak transcription	Fetal Intestine Small	intestine

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