Variant report

Variant	rs16874029
Chromosome Location	chr6:45918525-45918526
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs16874013	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16874019	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179992	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34943199	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35376655	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35570290	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3777562	1.00[MEX][hapmap]
rs3798264	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3798265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6916183	0.85[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6921488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71566554	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16874029	PER3	trans	lymphoblastoid	seeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45898800-45919200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr6:45908000-45918600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:45911000-45919200	Weak transcription	Small Intestine	intestine
4	chr6:45911000-45923600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:45911400-45919000	Weak transcription	Adipose Nuclei	Adipose
6	chr6:45912600-45923000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
7	chr6:45912800-45928400	Weak transcription	Spleen	Spleen
8	chr6:45913400-45919000	Strong transcription	Fetal Intestine Small	intestine
9	chr6:45913800-45920000	Enhancers	Placenta	Placenta
10	chr6:45914200-45919200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:45914600-45918800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:45914600-45919400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:45915000-45919200	Weak transcription	Lung	lung
14	chr6:45915200-45919000	Weak transcription	Right Atrium	heart
15	chr6:45915400-45919000	Weak transcription	Fetal Heart	heart
16	chr6:45915800-45918800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:45915800-45919800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr6:45916200-45919400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:45916800-45919000	Weak transcription	Right Ventricle	heart
20	chr6:45917200-45918800	Weak transcription	Fetal Intestine Large	intestine
21	chr6:45917200-45919000	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:45917200-45919000	Weak transcription	Left Ventricle	heart
23	chr6:45917200-45919000	Weak transcription	Pancreas	Pancrea
24	chr6:45917200-45919000	Weak transcription	Psoas Muscle	Psoas
25	chr6:45917200-45919200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:45917200-45919200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr6:45917200-45924800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr6:45917400-45918800	Weak transcription	Fetal Kidney	kidney
29	chr6:45917400-45919000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr6:45917400-45919000	Weak transcription	HSMMtube	muscle
31	chr6:45917400-45919200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:45918000-45918800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:45918000-45919000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr6:45918200-45920000	Enhancers	Colonic Mucosa	Colon

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