Variant report

Variant	rs414219
Chromosome Location	chr11:16900362-16900363
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:16898156..16901710-chr11:16902984..16905374,4	K562	blood:

Variant related genes	Relation type
ENSG00000166689	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10741713	0.94[JPT][hapmap]
rs10766360	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs11024087	0.93[JPT][hapmap]
rs12418111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1638456	0.93[ASN][1000 genomes]
rs1638457	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16933675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16933680	1.00[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.87[AFR][1000 genomes]
rs16933682	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes]
rs16933683	0.94[JPT][hapmap]
rs16933684	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs177544	1.00[CEU][hapmap]
rs177546	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs177551	0.83[ASN][1000 genomes]
rs177554	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs177561	0.94[JPT][hapmap]
rs177562	0.94[JPT][hapmap]
rs177563	0.88[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap]
rs1860024	0.82[JPT][hapmap]
rs2057788	0.94[JPT][hapmap]
rs2190752	0.94[JPT][hapmap]
rs2883150	0.94[JPT][hapmap]
rs35109048	0.87[AFR][1000 genomes]
rs367373	0.80[ASN][1000 genomes]
rs369457	0.94[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs370053	0.81[AMR][1000 genomes]
rs370671	0.81[AMR][1000 genomes]
rs371905	0.94[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs378863	0.95[ASN][1000 genomes]
rs381815	0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs382280	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs385627	0.81[AMR][1000 genomes]
rs387849	0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs388968	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs389967	0.88[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes]
rs390974	0.94[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs391332	0.92[ASN][1000 genomes]
rs393633	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs397343	0.94[JPT][hapmap]
rs397373	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs400085	0.94[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes]
rs400349	0.81[AMR][1000 genomes]
rs400458	0.94[JPT][hapmap]
rs401820	0.94[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs402982	0.88[JPT][hapmap]
rs406890	0.94[JPT][hapmap]
rs406937	0.81[AMR][1000 genomes]
rs407354	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs407932	0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs409354	1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs413858	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs414992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs416258	0.84[JPT][hapmap]
rs417406	0.88[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes]
rs420975	0.94[JPT][hapmap];0.81[TSI][hapmap]
rs422272	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs425325	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs425745	0.85[JPT][hapmap]
rs427429	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs428840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs428933	0.94[JPT][hapmap]
rs429368	0.81[AMR][1000 genomes]
rs430211	0.94[JPT][hapmap]
rs431208	0.94[JPT][hapmap]
rs432046	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs433212	0.94[JPT][hapmap]
rs433225	0.94[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs434761	0.94[JPT][hapmap]
rs434899	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs435206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs440212	0.94[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs443327	0.81[AMR][1000 genomes]
rs445146	0.93[JPT][hapmap]
rs445205	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs445431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs446518	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs446612	0.81[AMR][1000 genomes]
rs448671	0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs450828	0.94[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs452414	0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs452745	0.94[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs454869	0.94[JPT][hapmap]
rs4756875	0.88[CHD][hapmap];0.94[JPT][hapmap];0.81[MKK][hapmap]
rs4756876	0.88[CHD][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.81[MKK][hapmap]
rs4757449	0.88[CHD][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.93[MKK][hapmap]
rs4757451	0.94[JPT][hapmap]
rs4757452	0.93[JPT][hapmap]
rs4757454	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs4757456	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs4757457	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs58542530	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59828007	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61882035	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61882036	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61882037	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61882038	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6486326	0.94[JPT][hapmap]
rs7111470	0.94[JPT][hapmap]
rs7396552	0.80[CHD][hapmap];0.88[JPT][hapmap]
rs7481080	0.89[JPT][hapmap]
rs758402	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7924696	0.94[JPT][hapmap]
rs7926335	0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7939987	0.94[JPT][hapmap]

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	nsv832077	chr11:16834545-17059176	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs414219	PIK3C2A	cis	cerebellum	SCAN
rs414219	SAA1	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16885200-16902400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr11:16885400-16900800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:16891000-16900800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr11:16891000-16901000	Weak transcription	Lung	lung
5	chr11:16891200-16904600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr11:16891600-16903600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:16893400-16901600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:16893400-16902600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr11:16896400-16901800	Weak transcription	Fetal Intestine Large	intestine
10	chr11:16896600-16902400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr11:16896600-16902600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr11:16896800-16902600	Weak transcription	HSMMtube	muscle
13	chr11:16897200-16900400	Enhancers	Placenta Amnion	Placenta Amnion
14	chr11:16897400-16901200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr11:16897600-16901200	Enhancers	Brain Anterior Caudate	brain
16	chr11:16897800-16900400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr11:16897800-16901000	Weak transcription	Fetal Intestine Small	intestine
18	chr11:16898000-16903600	Enhancers	Gastric	stomach
19	chr11:16898400-16908400	Weak transcription	HepG2	liver
20	chr11:16898600-16900800	Weak transcription	Right Atrium	heart
21	chr11:16898800-16901600	Weak transcription	Ovary	ovary
22	chr11:16898800-16902400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr11:16898800-16902400	Weak transcription	Fetal Lung	lung
24	chr11:16898800-16902800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:16899000-16900600	Enhancers	Fetal Heart	heart
26	chr11:16899000-16902600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr11:16899000-16902600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:16899200-16900400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr11:16899200-16900800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:16899200-16902000	Weak transcription	NHEK	skin
31	chr11:16899200-16903000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr11:16899200-16903600	Enhancers	Left Ventricle	heart
33	chr11:16899400-16902600	Weak transcription	Brain Substantia Nigra	brain
34	chr11:16899400-16904600	Weak transcription	Placenta	Placenta
35	chr11:16899800-16900600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:16899800-16900800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr11:16899800-16900800	Weak transcription	HMEC	breast
38	chr11:16900000-16900600	Enhancers	H9 Cell Line	embryonic stem cell
39	chr11:16900000-16901200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr11:16900000-16902000	Enhancers	Right Ventricle	heart
41	chr11:16900000-16903600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr11:16900000-16903600	Enhancers	Pancreas	Pancrea
43	chr11:16900200-16900600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr11:16900200-16901800	Enhancers	Esophagus	oesophagus
45	chr11:16900200-16905400	Enhancers	Stomach Mucosa	stomach

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