Variant report

Variant	rs999323
Chromosome Location	chr17:45371603-45371604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45264504..45267447-chr17:45370883..45372399,2	K562	blood:
2	chr17:45369846..45373285-chr17:45374240..45379330,4	K562	blood:
3	chr17:45363175..45368028-chr17:45369299..45373237,4	K562	blood:
4	chr17:45368833..45371722-chr17:45375915..45378676,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000004897	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1000232	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10514919	0.82[TSI][hapmap]
rs11656809	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11657517	0.81[TSI][hapmap]
rs12949936	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs15908	0.81[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16941801	0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2015729	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs2292699	0.87[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2292863	0.90[CEU][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2292865	0.86[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3851807	0.87[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap]
rs4634	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4642	1.00[ASW][hapmap];0.90[CEU][hapmap];0.93[LWK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56327427	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7212751	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs7214468	0.82[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7217710	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7218632	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8073827	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[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	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs999323	KRT31	cis	parietal	SCAN
rs999323	HSS00008485	cis	multi-tissue	Pritchard
rs999323	NMT1	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45354600-45372000	Weak transcription	Esophagus	oesophagus
2	chr17:45356800-45377200	Weak transcription	Fetal Intestine Large	intestine
3	chr17:45357200-45398000	Weak transcription	Psoas Muscle	Psoas
4	chr17:45358200-45371800	Weak transcription	Colonic Mucosa	Colon
5	chr17:45358200-45377200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr17:45359000-45372000	Weak transcription	Left Ventricle	heart
7	chr17:45359000-45389800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr17:45360400-45371800	Strong transcription	Colon Smooth Muscle	Colon
9	chr17:45360600-45373800	Strong transcription	Fetal Stomach	stomach
10	chr17:45360800-45371800	Strong transcription	Fetal Muscle Leg	muscle
11	chr17:45364400-45371800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr17:45366200-45372200	Weak transcription	Small Intestine	intestine
13	chr17:45366400-45371800	Weak transcription	Lung	lung
14	chr17:45366600-45371800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr17:45366600-45371800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr17:45366600-45371800	Weak transcription	Right Atrium	heart
17	chr17:45366800-45371800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr17:45368200-45372800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr17:45368600-45372800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr17:45369400-45373000	Enhancers	K562	blood
21	chr17:45369600-45373600	Strong transcription	Placenta	Placenta
22	chr17:45369800-45373400	Enhancers	Primary B cells from peripheral blood	blood
23	chr17:45370000-45371800	Weak transcription	Aorta	Aorta
24	chr17:45370000-45371800	Weak transcription	Ovary	ovary
25	chr17:45370000-45371800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr17:45370000-45372000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr17:45370000-45372000	Weak transcription	Spleen	Spleen
28	chr17:45370000-45376600	Weak transcription	Pancreas	Pancrea
29	chr17:45370000-45378000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr17:45370200-45372000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr17:45370600-45372600	Enhancers	Primary B cells from cord blood	blood
32	chr17:45370800-45371800	Enhancers	Adipose Nuclei	Adipose
33	chr17:45371000-45377200	Weak transcription	Fetal Heart	heart
34	chr17:45371200-45372000	Enhancers	Osteobl	bone
35	chr17:45371200-45372600	Enhancers	NH-A	brain
36	chr17:45371200-45372800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr17:45371200-45374000	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr17:45371200-45374000	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr17:45371400-45371800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr17:45371400-45372200	Enhancers	GM12878-XiMat	blood
41	chr17:45371400-45372600	Enhancers	Liver	Liver
42	chr17:45371400-45372600	Enhancers	HMEC	breast
43	chr17:45371400-45372600	Enhancers	NHDF-Ad	bronchial
44	chr17:45371400-45372800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr17:45371400-45372800	Enhancers	Muscle Satellite Cultured Cells	--
46	chr17:45371400-45372800	Enhancers	HSMMtube	muscle
47	chr17:45371400-45374400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr17:45371400-45374400	Enhancers	Brain Hippocampus Middle	brain
49	chr17:45371400-45393000	Weak transcription	Dnd41	blood
50	chr17:45371600-45371800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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