Variant report

Variant	rs11161515
Chromosome Location	chr1:76212559-76212560
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:76212436-76213481	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:76203557..76205358-chr1:76211524..76214025,2	K562	blood:
2	chr1:76199593..76201164-chr1:76211296..76213584,2	K562	blood:
3	chr1:76190391..76191976-chr1:76212082..76213734,2	K562	blood:
4	chr1:76189028..76194220-chr1:76209012..76215464,6	K562	blood:
5	chr1:76205678..76212783-chr1:76212896..76217702,9	K562	blood:
6	chr1:76198750..76201093-chr1:76210401..76212796,3	K562	blood:

No data

Variant related genes	Relation type
ACADM	TF binding region
ENSG00000181227	TF binding region
ENSG00000178193	Chromatin interaction
ENSG00000117054	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1061337	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873685	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161437	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11161468	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161493	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161510	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161511	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161521	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161620	0.80[AMR][1000 genomes]
rs11163924	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1146574	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146579	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146580	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146581	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146588	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091720	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12093623	0.80[AMR][1000 genomes]
rs12094842	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12123977	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126481	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126607	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127402	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134854	0.84[EUR][1000 genomes]
rs12136754	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250874	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251075	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1303169	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1313071	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498312	0.94[EUR][1000 genomes]
rs1498315	0.92[EUR][1000 genomes]
rs1498316	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1498317	0.85[EUR][1000 genomes]
rs1611823	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1612097	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1694419	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1694424	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17587071	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767455	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767456	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767458	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770511	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1855136	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1858536	0.86[EUR][1000 genomes]
rs1890451	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890452	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066183	0.84[EUR][1000 genomes]
rs211737	0.80[AMR][1000 genomes]
rs2153126	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173378	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185152	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2185435	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185436	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211080	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2275378	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788654	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28602663	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3818855	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392691	0.80[AMR][1000 genomes]
rs4559448	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646961	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949674	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949872	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4949874	0.92[EUR][1000 genomes]
rs4949875	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4949876	0.93[EUR][1000 genomes]
rs4949877	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949879	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56267813	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56352044	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57186386	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60378926	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61289992	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61622554	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61797339	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61797340	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61799967	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61799988	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61799990	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6593514	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593515	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593585	0.86[EUR][1000 genomes]
rs6688749	0.89[EUR][1000 genomes]
rs72686191	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7513363	0.82[EUR][1000 genomes]
rs7513559	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7516122	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7516226	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7518038	0.90[EUR][1000 genomes]
rs7524467	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533888	0.91[EUR][1000 genomes]
rs7534754	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7535991	0.86[EUR][1000 genomes]
rs7539246	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541058	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544117	0.86[EUR][1000 genomes]
rs7546641	0.85[EUR][1000 genomes]
rs7548962	0.86[EUR][1000 genomes]
rs7549167	0.86[EUR][1000 genomes]
rs7550974	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552404	0.86[EUR][1000 genomes]
rs7554984	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8763	0.93[ASN][1000 genomes]
rs942270	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9662166	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11161515	MSH4	cis	Artery Tibial	GTEx
rs11161515	ACADM	cis	Whole Blood	GTEx
rs11161515	ACADM	cis	Esophagus Muscularis	GTEx
rs11161515	MSH4	cis	Esophagus Muscularis	GTEx
rs11161515	ACADM	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76191200-76219600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:76192000-76220400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:76192000-76220600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:76192000-76227800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:76192200-76217800	Weak transcription	Fetal Brain Male	brain
6	chr1:76192200-76222000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:76193600-76220200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:76193800-76220200	Weak transcription	Fetal Heart	heart
9	chr1:76195600-76219600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:76195800-76213800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:76196000-76222000	Strong transcription	Liver	Liver
12	chr1:76196200-76212600	Strong transcription	Fetal Thymus	thymus
13	chr1:76196400-76213000	Strong transcription	Dnd41	blood
14	chr1:76197600-76219400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:76199600-76218600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:76199600-76220400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:76201600-76217800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:76202000-76225000	Weak transcription	Stomach Mucosa	stomach
19	chr1:76203400-76230800	Weak transcription	NHDF-Ad	bronchial
20	chr1:76204800-76229000	Weak transcription	Psoas Muscle	Psoas
21	chr1:76208600-76223800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:76208800-76216200	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:76208800-76220400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:76208800-76231400	Weak transcription	A549	lung
25	chr1:76208800-76231400	Weak transcription	NHEK	skin
26	chr1:76208800-76231600	Weak transcription	Hela-S3	cervix
27	chr1:76209000-76214000	Weak transcription	HSMM	muscle
28	chr1:76209000-76216000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:76209000-76220200	Weak transcription	Fetal Kidney	kidney
30	chr1:76209000-76230800	Weak transcription	HUVEC	blood vessel
31	chr1:76209000-76230800	Weak transcription	NHLF	lung
32	chr1:76209200-76216600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:76209400-76217600	Weak transcription	HepG2	liver
34	chr1:76209400-76220400	Weak transcription	Colonic Mucosa	Colon
35	chr1:76209600-76216000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:76209600-76216000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:76210000-76215800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:76210000-76218600	Weak transcription	Small Intestine	intestine
39	chr1:76210200-76215600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:76210200-76215800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:76210200-76215800	Weak transcription	Placenta	Placenta
42	chr1:76210200-76216000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:76210200-76217000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr1:76210200-76217200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:76210200-76217600	Weak transcription	Primary B cells from cord blood	blood
46	chr1:76210200-76217600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:76210200-76220200	Weak transcription	Right Ventricle	heart
48	chr1:76210200-76220400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr1:76210200-76223000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr1:76210200-76231800	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links