Variant report

Variant	rs16890522
Chromosome Location	chr6:38236302-38236303
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	chr6:38230666..38232627-chr6:38236052..38240073,5	MCF-7	breast:
2	chr6:38231064..38233910-chr6:38235899..38238476,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10484933	1.00[CHB][hapmap]
rs12524219	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12526138	1.00[AFR][1000 genomes]
rs12529300	0.86[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12529640	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs16890465	1.00[CHB][hapmap]
rs16890468	1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs16890511	1.00[CHB][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes]
rs4711526	0.86[CHB][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4711530	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4711534	0.80[CHD][hapmap]
rs4714127	1.00[AFR][1000 genomes]
rs4714135	1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4714137	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4714142	1.00[AFR][1000 genomes]
rs62397007	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62397011	0.83[AMR][1000 genomes]
rs62397015	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6929505	1.00[CHB][hapmap]
rs7739762	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs872234	0.80[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16890522	EGR2	trans	brain	seeQTL
rs16890522	PTGS2	trans	brain	seeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38208200-38236600	Weak transcription	Gastric	stomach
2	chr6:38208200-38255000	Weak transcription	Ovary	ovary
3	chr6:38216000-38238000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:38220000-38238200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:38220600-38241600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:38223600-38256000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:38224400-38239000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:38224400-38267600	Weak transcription	Primary T cells from cord blood	blood
9	chr6:38224600-38255200	Weak transcription	Primary B cells from cord blood	blood
10	chr6:38224800-38256400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:38225000-38255800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr6:38225200-38238600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:38225800-38238400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:38225800-38239200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr6:38226400-38258000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:38226600-38256600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:38226600-38257000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:38230200-38237400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:38230200-38253400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr6:38230400-38237200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:38230400-38237200	Weak transcription	Fetal Stomach	stomach
22	chr6:38230400-38237400	Weak transcription	Aorta	Aorta
23	chr6:38230800-38236600	Weak transcription	Left Ventricle	heart
24	chr6:38230800-38237400	Weak transcription	Fetal Brain Female	brain
25	chr6:38230800-38238000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:38230800-38241200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr6:38230800-38256000	Weak transcription	Right Atrium	heart
28	chr6:38230800-38257800	Weak transcription	Pancreas	Pancrea
29	chr6:38231000-38250800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:38231600-38237200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:38232200-38237200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:38232200-38237400	Weak transcription	NHLF	lung
33	chr6:38232600-38237400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:38232800-38236600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr6:38232800-38238000	Weak transcription	Right Ventricle	heart
36	chr6:38232800-38241200	Weak transcription	Small Intestine	intestine
37	chr6:38233000-38237200	Weak transcription	Fetal Heart	heart
38	chr6:38233400-38236600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:38233800-38241800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr6:38234400-38241600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:38234600-38236800	Enhancers	Brain Anterior Caudate	brain
42	chr6:38234600-38238200	Enhancers	Brain Angular Gyrus	brain
43	chr6:38234600-38238400	Enhancers	Brain Germinal Matrix	brain
44	chr6:38234600-38238600	Enhancers	Brain Cingulate Gyrus	brain
45	chr6:38234600-38238600	Enhancers	Brain Hippocampus Middle	brain
46	chr6:38234600-38238600	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr6:38234800-38237400	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr6:38234800-38238800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr6:38235000-38237200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:38235000-38237200	Weak transcription	Osteobl	bone

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