Variant report

Variant	rs10742177
Chromosome Location	chr11:3853146-3853147
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:54)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:54 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr11:3852744-3853441	K562	blood:	n/a	n/a
2	MAX	chr11:3852891-3853438	K562	blood:	n/a	chr11:3852944-3852954
3	POLR2A	chr11:3852726-3854044	K562	blood:	n/a	n/a
4	POLR2A	chr11:3852379-3853448	GM12892	blood:	n/a	n/a
5	GATA1	chr11:3852529-3853700	K562	blood:	n/a	n/a
6	REST	chr11:3852965-3853351	K562	blood:	n/a	n/a
7	UBTF	chr11:3852855-3853402	K562	blood:	n/a	n/a
8	POLR2A	chr11:3853134-3854126	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr11:3852336-3853411	K562	blood:	n/a	n/a
10	RCOR1	chr11:3852908-3853475	K562	blood:	n/a	n/a
11	RCOR1	chr11:3853048-3853367	K562	blood:	n/a	n/a
12	TAL1	chr11:3853025-3853262	K562	blood:	n/a	n/a
13	POLR2A	chr11:3853008-3854121	GM12878	blood:	n/a	n/a
14	GATA2	chr11:3852980-3853369	K562	blood:	n/a	n/a
15	HCFC1	chr11:3853070-3853339	K562	blood:	n/a	n/a
16	ARID3A	chr11:3852926-3853495	K562	blood:	n/a	n/a
17	HDAC2	chr11:3852917-3853275	K562	blood:	n/a	n/a
18	POLR2A	chr11:3852548-3853806	GM12878	blood:	n/a	n/a
19	POLR2A	chr11:3853090-3853897	K562	blood:	n/a	n/a
20	ELF1	chr11:3852896-3853403	K562	blood:	n/a	n/a
21	JUND	chr11:3852749-3853558	K562	blood:	n/a	n/a
22	ZC3H11A	chr11:3852902-3853374	K562	blood:	n/a	n/a
23	ZNF143	chr11:3852881-3853389	K562	blood:	n/a	n/a
24	MAZ	chr11:3852907-3853380	K562	blood:	n/a	chr11:3852944-3852954
25	POLR2A	chr11:3852069-3854235	K562	blood:	n/a	n/a
26	UBTF	chr11:3852945-3853294	K562	blood:	n/a	n/a
27	EGR1	chr11:3852860-3853186	K562	blood:	n/a	n/a
28	PML	chr11:3852765-3853382	K562	blood:	n/a	n/a
29	NR2F2	chr11:3852980-3853550	K562	blood:	n/a	chr11:3853375-3853390
30	SPI1	chr11:3852853-3853355	HL-60	blood:	n/a	n/a
31	POLR2A	chr11:3852687-3855224	GM12878	blood:	n/a	n/a
32	TBL1XR1	chr11:3852771-3853238	K562	blood:	n/a	n/a
33	EP300	chr11:3852795-3853443	K562	blood:	n/a	n/a
34	MAFK	chr11:3852807-3853234	K562	blood:	n/a	n/a
35	ZNF384	chr11:3852992-3853239	K562	blood:	n/a	n/a
36	POLR2A	chr11:3851901-3854284	HL-60	blood:	n/a	n/a
37	CUX1	chr11:3853050-3853445	K562	blood:	n/a	n/a
38	BHLHE40	chr11:3852921-3853716	K562	blood:	n/a	n/a
39	ZMIZ1	chr11:3852986-3853247	K562	blood:	n/a	n/a
40	POLR2A	chr11:3853129-3853644	GM12892	blood:	n/a	n/a
41	MAX	chr11:3852963-3853412	K562	blood:	n/a	n/a
42	MYC	chr11:3852966-3853440	K562	blood:	n/a	n/a
43	EGR1	chr11:3852924-3853174	K562	blood:	n/a	n/a
44	ATF1	chr11:3852932-3853381	K562	blood:	n/a	n/a
45	POLR2A	chr11:3851880-3854822	HL-60	blood:	n/a	n/a
46	POLR2A	chr11:3852874-3853355	K562	blood:	n/a	n/a
47	CBX3	chr11:3852830-3853547	K562	blood:	n/a	n/a
48	POLR2A	chr11:3852599-3853404	K562	blood:	n/a	n/a
49	MAFF	chr11:3852776-3853325	K562	blood:	n/a	n/a
50	SPI1	chr11:3852966-3853269	K562	blood:	n/a	n/a

No data

Variant related genes	Relation type
RHOG	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1055639	0.81[JPT][hapmap]
rs10835174	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10835175	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10835177	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10835178	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11030002	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11030008	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12363789	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1451720	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1451721	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1451722	0.81[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap]
rs4597058	0.81[JPT][hapmap]
rs962199	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1038220	chr11:3818041-3860024	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv1044882	chr11:3828986-3860024	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv1044360	chr11:3832288-3860024	Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10742177	PSMD13	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3830600-3861000	Weak transcription	Fetal Kidney	kidney
2	chr11:3842000-3853600	Strong transcription	Fetal Intestine Small	intestine
3	chr11:3844000-3857000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:3844400-3856200	Strong transcription	Fetal Stomach	stomach
5	chr11:3844600-3853400	Strong transcription	Thymus	Thymus
6	chr11:3844800-3854800	Strong transcription	Dnd41	blood
7	chr11:3844800-3857000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:3845000-3856000	Weak transcription	HUVEC	blood vessel
9	chr11:3845200-3855800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr11:3845400-3854200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:3845400-3855000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:3845400-3855800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:3845600-3855800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:3846000-3853800	Strong transcription	A549	lung
15	chr11:3846400-3855000	Strong transcription	NHEK	skin
16	chr11:3848400-3853200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:3848400-3861000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:3848600-3853200	Weak transcription	Stomach Mucosa	stomach
19	chr11:3848600-3858200	Weak transcription	NHDF-Ad	bronchial
20	chr11:3848800-3855400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:3849200-3853600	Weak transcription	HepG2	liver
22	chr11:3849200-3855400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr11:3849400-3853600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr11:3849400-3853600	Weak transcription	Colonic Mucosa	Colon
25	chr11:3849400-3855800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr11:3849400-3855800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr11:3849400-3856000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr11:3849400-3856000	Weak transcription	Brain Germinal Matrix	brain
29	chr11:3849400-3859000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:3849600-3853600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr11:3849600-3855600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr11:3849600-3855600	Weak transcription	Colon Smooth Muscle	Colon
33	chr11:3849600-3855800	Weak transcription	Aorta	Aorta
34	chr11:3849600-3856400	Weak transcription	Ovary	ovary
35	chr11:3849600-3861000	Weak transcription	HSMMtube	muscle
36	chr11:3849800-3854600	Weak transcription	Hela-S3	cervix
37	chr11:3849800-3854800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr11:3849800-3855400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr11:3849800-3855800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:3849800-3856200	Weak transcription	HSMM	muscle
41	chr11:3850200-3853200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr11:3850200-3853200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
43	chr11:3850200-3855000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:3850400-3855600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr11:3850600-3855600	Genic enhancers	Primary T cells fromperipheralblood	blood
46	chr11:3851200-3853800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr11:3851400-3853200	Genic enhancers	Primary hematopoietic stem cells	blood
48	chr11:3851400-3853400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr11:3851400-3853400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr11:3851400-3853600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links