Variant report

Variant	rs11161626
Chromosome Location	chr1:76260837-76260838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:67)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:67 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:76260800-76263815	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:76249993-76263987	K562	blood:	n/a	n/a
3	POLR2A	chr1:76260504-76263958	K562	blood:	n/a	n/a
4	POLR2A	chr1:76257827-76264091	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:76260673-76263240	A549	lung:	n/a	n/a
6	MBD4	chr1:76260505-76260871	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:76260664-76263724	H1-hESC	embryonic stem cell:	n/a	n/a
8	TEAD4	chr1:76260755-76263209	K562	blood:	n/a	n/a
9	POLR2A	chr1:76250010-76263479	K562	blood:	n/a	n/a
10	POLR2A	chr1:76250991-76264029	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr1:76260562-76263803	GM12892	blood:	n/a	n/a
12	POLR2A	chr1:76260648-76263840	PBDE	blood:	n/a	n/a
13	POLR2A	chr1:76260472-76264653	U87	brain:	n/a	n/a
14	POLR2A	chr1:76250033-76264125	K562	blood:	n/a	n/a
15	POLR2A	chr1:76260357-76263709	GM12892	blood:	n/a	n/a
16	POLR2A	chr1:76260821-76263271	K562	blood:	n/a	n/a
17	POLR2A	chr1:76260636-76263660	GM18526	blood:	n/a	n/a
18	POLR2A	chr1:76260796-76263772	GM12892	blood:	n/a	n/a
19	POLR2A	chr1:76260630-76261138	IMR90	lung:	n/a	n/a
20	POLR2A	chr1:76257887-76264164	HepG2	liver:	n/a	n/a
21	ZNF384	chr1:76260682-76261221	K562	blood:	n/a	n/a
22	MTA3	chr1:76260796-76263989	GM12878	blood:	n/a	n/a
23	PML	chr1:76260551-76262989	K562	blood:	n/a	n/a
24	POLR2A	chr1:76260828-76263740	GM12878	blood:	n/a	n/a
25	CCNT2	chr1:76260727-76263194	K562	blood:	n/a	n/a
26	POLR2A	chr1:76257762-76263752	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:76260587-76260867	H1-hESC	embryonic stem cell:	n/a	n/a
28	PML	chr1:76260836-76263375	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:76258764-76263332	GM19099	blood:	n/a	n/a
30	POLR2A	chr1:76260605-76260873	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr1:76260508-76263839	HL-60	blood:	n/a	n/a
32	POLR2A	chr1:76250068-76266595	GM12878	blood:	n/a	n/a
33	MBD4	chr1:76260563-76263333	HepG2	liver:	n/a	n/a
34	POLR2A	chr1:76260454-76260979	U87	brain:	n/a	n/a
35	POLR2A	chr1:76260699-76264204	HUVEC	blood vessel:	n/a	n/a
36	PML	chr1:76260592-76263309	K562	blood:	n/a	n/a
37	POLR2A	chr1:76260454-76261022	U87	brain:	n/a	n/a
38	NFIC	chr1:76260815-76263268	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:76250047-76263901	GM18505	blood:	n/a	n/a
40	POLR2A	chr1:76249945-76266639	GM12891	blood:	n/a	n/a
41	POLR2A	chr1:76250036-76264085	K562	blood:	n/a	n/a
42	POLR2A	chr1:76260454-76263763	K562	blood:	n/a	n/a
43	POLR2A	chr1:76260549-76263160	K562	blood:	n/a	n/a
44	EP300	chr1:76260709-76260941	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:76256643-76264175	HepG2	liver:	n/a	n/a
46	POLR2A	chr1:76260805-76263197	K562	blood:	n/a	n/a
47	POLR2A	chr1:76260616-76263940	GM18951	blood:	n/a	n/a
48	POLR2A	chr1:76260509-76263850	GM12892	blood:	n/a	n/a
49	POLR2A	chr1:76259072-76264143	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr1:76257012-76263648	PFSK-1	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:76252156..76254487-chr1:76258379..76261694,3	MCF-7	breast:
2	chr1:75819174..75821466-chr1:76259462..76262137,2	K562	blood:
3	chr1:76260266..76263027-chr1:76396916..76399571,2	K562	blood:
4	chr1:76213109..76217378-chr1:76260068..76263795,4	K562	blood:
5	chr1:76257416..76260329-chr1:76260481..76263578,4	MCF-7	breast:
6	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
7	chr1:76200281..76202966-chr1:76259715..76263170,3	K562	blood:
8	chr1:76188764..76194417-chr1:76259356..76264333,14	K562	blood:
9	chr1:76196771..76202637-chr1:76258126..76262356,7	K562	blood:

No data

Variant related genes	Relation type
MSH4	TF binding region
ENSG00000178193	Chromatin interaction
ENSG00000207241	Chromatin interaction
ENSG00000206620	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000117054	Chromatin interaction
ENSG00000154007	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10782558	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161620	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161792	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1144336	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146646	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146653	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12021855	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12093623	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094842	0.84[EUR][1000 genomes]
rs12122939	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127078	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136360	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568447	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12723575	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1565717	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029681	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2029683	0.80[EUR][1000 genomes]
rs2172507	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2172508	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211080	0.86[EUR][1000 genomes]
rs2347962	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28602663	0.81[EUR][1000 genomes]
rs2881786	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4949677	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949879	0.81[EUR][1000 genomes]
rs4949885	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56267813	0.82[EUR][1000 genomes]
rs56352044	0.80[EUR][1000 genomes]
rs5745336	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745363	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745381	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5745390	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5745427	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5745433	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61770533	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61799990	0.85[EUR][1000 genomes]
rs6678348	0.85[EUR][1000 genomes]
rs7516226	0.81[EUR][1000 genomes]
rs7538800	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7547056	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549863	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9662166	0.81[EUR][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	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	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
3	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11161626	ACADM	cis	Whole Blood	GTEx
rs11161626	MSH4	cis	Esophagus Muscularis	GTEx
rs11161626	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL
rs11161626	MSH4	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76254200-76263200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:76254400-76262400	Strong transcription	Placenta	Placenta
3	chr1:76254400-76265200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr1:76254800-76262400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:76254800-76262600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:76255200-76261400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:76255200-76263600	Strong transcription	Fetal Lung	lung
8	chr1:76255400-76262600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:76255400-76263000	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr1:76255400-76265200	Weak transcription	Right Atrium	heart
11	chr1:76255600-76263000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:76255600-76264000	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr1:76255800-76261600	Weak transcription	Fetal Heart	heart
14	chr1:76255800-76264000	Strong transcription	Brain Anterior Caudate	brain
15	chr1:76255800-76264200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:76255800-76264200	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:76255800-76264400	Strong transcription	Fetal Muscle Leg	muscle
18	chr1:76256000-76262400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:76256000-76262800	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:76256000-76264200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:76256000-76264200	Strong transcription	Fetal Thymus	thymus
22	chr1:76256000-76264400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:76256000-76264400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:76256000-76264600	Strong transcription	Fetal Stomach	stomach
25	chr1:76256200-76262600	Strong transcription	Fetal Kidney	kidney
26	chr1:76256200-76263000	Strong transcription	Ovary	ovary
27	chr1:76256400-76262400	Strong transcription	Fetal Brain Female	brain
28	chr1:76256400-76262800	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:76256400-76262800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:76256400-76264400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:76256600-76261600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:76256600-76262400	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:76256600-76262600	Strong transcription	Primary B cells from cord blood	blood
34	chr1:76256600-76262600	Strong transcription	HMEC	breast
35	chr1:76256600-76263000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:76256600-76263000	Strong transcription	Colon Smooth Muscle	Colon
37	chr1:76256600-76263200	Strong transcription	Brain Angular Gyrus	brain
38	chr1:76256600-76263200	Strong transcription	Rectal Smooth Muscle	rectum
39	chr1:76256600-76263200	Strong transcription	NHLF	lung
40	chr1:76256600-76263400	Strong transcription	Adipose Nuclei	Adipose
41	chr1:76256600-76263400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr1:76256600-76264000	Strong transcription	Primary hematopoietic stem cells	blood
43	chr1:76256600-76264000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:76256600-76264200	Strong transcription	Brain Cingulate Gyrus	brain
45	chr1:76256600-76264600	Strong transcription	Primary B cells from peripheral blood	blood
46	chr1:76256600-76265000	Strong transcription	Primary T cells from cord blood	blood
47	chr1:76256800-76261000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:76256800-76261000	Weak transcription	Small Intestine	intestine
49	chr1:76256800-76262200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:76256800-76262400	Strong transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links