Variant report

Variant	rs390974
Chromosome Location	chr11:16848077-16848078
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	chr11:16847181..16850081-chr11:17095305..17097165,2	K562	blood:

Variant related genes	Relation type
ENSG00000110700	Chromatin interaction
ENSG00000221322	Chromatin interaction
ENSG00000272034	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10741713	0.88[JPT][hapmap]
rs10766360	0.88[JPT][hapmap]
rs11024087	0.87[JPT][hapmap]
rs12418111	0.88[JPT][hapmap]
rs1638457	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16933675	0.88[CHB][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs16933680	0.88[JPT][hapmap]
rs16933682	0.88[JPT][hapmap]
rs16933683	0.88[JPT][hapmap]
rs16933684	0.88[JPT][hapmap]
rs177561	0.88[JPT][hapmap]
rs177562	0.88[JPT][hapmap]
rs177563	0.88[JPT][hapmap]
rs2057788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2190752	0.88[JPT][hapmap]
rs2883150	0.88[JPT][hapmap]
rs369457	1.00[ASW][hapmap];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs370053	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs370671	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs371905	1.00[ASW][hapmap];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373266	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs376641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs378863	0.82[AMR][1000 genomes]
rs379051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs380655	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs381815	0.94[JPT][hapmap]
rs382280	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385627	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs385943	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs387849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388968	0.86[JPT][hapmap]
rs389967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs392706	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs393633	0.91[CEU][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs397343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs397373	0.91[CEU][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs398216	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs400085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs400349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs400458	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs401820	1.00[ASW][hapmap];1.00[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];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs402982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404492	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs406109	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs406890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs406937	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs407354	0.91[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs407932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409354	1.00[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs414219	0.94[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs414992	0.94[JPT][hapmap]
rs415265	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs417349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs417406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs418034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425325	0.91[CEU][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs425745	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs426085	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs428840	0.94[JPT][hapmap]
rs428933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429368	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs430211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs431208	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs432046	0.91[CEU][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap]
rs432656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs433212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs433225	1.00[ASW][hapmap];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434899	0.87[JPT][hapmap]
rs435206	0.93[JPT][hapmap]
rs439224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs440212	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs443327	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs445205	0.91[CEU][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs446518	0.90[CEU][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs446612	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs448671	0.94[JPT][hapmap]
rs450828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs452414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs452745	1.00[ASW][hapmap];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs453015	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs454538	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs454869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4756875	0.88[JPT][hapmap]
rs4756876	0.88[JPT][hapmap]
rs4757449	0.88[JPT][hapmap]
rs4757451	0.88[JPT][hapmap]
rs4757452	0.87[JPT][hapmap]
rs4757454	0.88[JPT][hapmap]
rs4757456	0.88[JPT][hapmap]
rs4757457	0.88[JPT][hapmap]
rs58555284	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6486314	0.83[YRI][hapmap]
rs6486326	0.88[JPT][hapmap]
rs7111470	0.88[JPT][hapmap]
rs7396552	0.83[JPT][hapmap]
rs7481080	0.83[JPT][hapmap]
rs7924696	0.88[JPT][hapmap]
rs7926335	0.88[JPT][hapmap]
rs7939987	0.88[JPT][hapmap]
rs7951328	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	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
rs390974	SAA1	cis	parietal	SCAN
rs390974	PTPN5	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16813200-16871400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr11:16823000-16871400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:16836000-16861600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr11:16837200-16848600	Weak transcription	Brain Germinal Matrix	brain
5	chr11:16839200-16878800	Weak transcription	Thymus	Thymus
6	chr11:16842400-16862200	Weak transcription	Fetal Kidney	kidney
7	chr11:16842600-16852600	Weak transcription	Placenta	Placenta
8	chr11:16842600-16853600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr11:16842600-16854200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr11:16842600-16855000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:16842600-16873400	Weak transcription	Hela-S3	cervix
12	chr11:16842800-16862200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr11:16843000-16874600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:16844000-16862000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:16844400-16861200	Weak transcription	HMEC	breast
16	chr11:16844600-16848400	Strong transcription	Fetal Intestine Large	intestine
17	chr11:16845000-16850600	Genic enhancers	Fetal Heart	heart
18	chr11:16845800-16848400	Strong transcription	Fetal Intestine Small	intestine
19	chr11:16845800-16855200	Strong transcription	HepG2	liver
20	chr11:16846000-16850600	Strong transcription	Liver	Liver
21	chr11:16846200-16849000	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr11:16846200-16849200	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr11:16846200-16857800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:16846400-16848200	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr11:16846400-16848200	Enhancers	Left Ventricle	heart
26	chr11:16846400-16852800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr11:16846600-16848200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr11:16846600-16848200	Genic enhancers	Ovary	ovary
29	chr11:16846600-16874000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr11:16846800-16849200	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr11:16846800-16850800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:16847000-16848200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:16847000-16848200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:16847000-16864000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr11:16847000-16871200	Weak transcription	Brain Substantia Nigra	brain
36	chr11:16847200-16848200	Genic enhancers	Duodenum Mucosa	Duodenum
37	chr11:16847200-16871400	Weak transcription	Brain Hippocampus Middle	brain
38	chr11:16847400-16848200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:16847400-16848200	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:16847400-16848200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr11:16847400-16848200	Strong transcription	Aorta	Aorta
42	chr11:16847400-16848200	Genic enhancers	Esophagus	oesophagus
43	chr11:16847400-16848200	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr11:16847400-16848200	Strong transcription	A549	lung
45	chr11:16847400-16848400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr11:16847400-16848600	Strong transcription	Pancreas	Pancrea
47	chr11:16847400-16849600	Enhancers	Stomach Mucosa	stomach
48	chr11:16847600-16848200	Enhancers	Right Ventricle	heart
49	chr11:16847600-16848200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr11:16847600-16848200	Strong transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links