Variant report

Variant	rs3768371
Chromosome Location	chr1:226833608-226833609
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	chr1:226832724..226834932-chr1:226836674..226839333,2	MCF-7	breast:
2	chr1:226827940..226829963-chr1:226831824..226834705,3	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12077348	0.86[ASW][hapmap];0.86[GIH][hapmap]
rs12405164	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12568026	0.81[CHB][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2236604	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35483910	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3729551	0.85[CEU][hapmap]
rs3738723	1.00[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs3754380	0.92[CEU][hapmap];0.95[GIH][hapmap];0.82[EUR][1000 genomes]
rs3754387	0.81[ASW][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3768372	0.81[ASW][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3768373	0.93[ASW][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3820636	0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[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	nsv873234	chr1:226779449-226859676	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv873235	chr1:226819073-226851963	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3768371	TLR5	cis	parietal	SCAN
rs3768371	PARP1	cis	cerebellum	SCAN
rs3768371	DUSP5P	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226814200-226837600	Weak transcription	HUVEC	blood vessel
2	chr1:226814800-226834800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:226814800-226840600	Weak transcription	Small Intestine	intestine
4	chr1:226816800-226837000	Weak transcription	Fetal Brain Male	brain
5	chr1:226817000-226837000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:226820400-226840800	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr1:226823200-226834800	Weak transcription	Fetal Kidney	kidney
8	chr1:226823200-226841400	Weak transcription	NHDF-Ad	bronchial
9	chr1:226823400-226834400	Genic enhancers	Fetal Muscle Trunk	muscle
10	chr1:226823800-226837400	Strong transcription	Dnd41	blood
11	chr1:226824000-226834800	Genic enhancers	Fetal Muscle Leg	muscle
12	chr1:226824800-226836800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:226825000-226834200	Weak transcription	Liver	Liver
14	chr1:226825800-226834000	Genic enhancers	Brain Anterior Caudate	brain
15	chr1:226828000-226837200	Genic enhancers	Brain Hippocampus Middle	brain
16	chr1:226829200-226834800	Genic enhancers	Brain Cingulate Gyrus	brain
17	chr1:226829400-226843800	Weak transcription	Brain Germinal Matrix	brain
18	chr1:226829600-226835000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:226829800-226834800	Weak transcription	Aorta	Aorta
20	chr1:226830000-226834800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:226830200-226834400	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr1:226830200-226834800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:226830400-226834200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:226830400-226834200	Genic enhancers	Thymus	Thymus
25	chr1:226830400-226834400	Genic enhancers	Fetal Stomach	stomach
26	chr1:226830400-226834400	Enhancers	Placenta Amnion	Placenta Amnion
27	chr1:226830400-226834800	Genic enhancers	Fetal Thymus	thymus
28	chr1:226830400-226835600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:226830400-226840400	Genic enhancers	Primary T cells from cord blood	blood
30	chr1:226830400-226840400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
31	chr1:226830600-226834600	Genic enhancers	Esophagus	oesophagus
32	chr1:226830600-226835000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:226830600-226835000	Genic enhancers	Colon Smooth Muscle	Colon
34	chr1:226830600-226835800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:226830600-226838000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:226830800-226833800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:226830800-226835000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:226831000-226834000	Genic enhancers	Colonic Mucosa	Colon
39	chr1:226831000-226834800	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr1:226831200-226834400	Genic enhancers	Right Ventricle	heart
41	chr1:226831200-226837400	Genic enhancers	Brain Substantia Nigra	brain
42	chr1:226831400-226841600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:226831600-226834400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:226831600-226834400	Weak transcription	Ovary	ovary
45	chr1:226831600-226835200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:226831600-226835200	Weak transcription	NHEK	skin
47	chr1:226831800-226834000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:226831800-226834400	Genic enhancers	Placenta	Placenta
49	chr1:226831800-226835000	Genic enhancers	Lung	lung
50	chr1:226831800-226837000	Strong transcription	Fetal Intestine Small	intestine

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