Variant report

Variant	rs1783828
Chromosome Location	chr11:57411521-57411522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:69)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:69 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr11:57411436-57411591	MCF10A-Er-Src	breast:	n/a	chr11:57411540-57411550
2	MYC	chr11:57411350-57411551	MCF10A-Er-Src	breast:	n/a	chr11:57411540-57411550
3	CTCF	chr11:57411431-57411547	MCF-7	breast:	n/a	n/a
4	CTCF	chr11:57411380-57411530	BJ	skin:	n/a	n/a
5	CTCF	chr11:57411420-57411570	NHEK	skin:	n/a	n/a
6	POLR2A	chr11:57410796-57421100	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr11:57411520-57411670	HAc	cerebellar:	n/a	n/a
8	POLR2A	chr11:57411268-57411593	HepG2	liver:	n/a	n/a
9	POLR2A	chr11:57404829-57418710	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr11:57410916-57411627	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr11:57410821-57420904	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr11:57411268-57411544	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr11:57411396-57411650	K562	blood:	n/a	chr11:57411540-57411550
14	CTCF	chr11:57411400-57411550	HA-sp	spinal cord:	n/a	n/a
15	CTCF	chr11:57411440-57411590	HCM	heart:	n/a	n/a
16	CTCF	chr11:57411440-57411590	HCT-116	colon:	n/a	n/a
17	CTCF	chr11:57411380-57411530	AG09319	gingival:	n/a	n/a
18	CTCF	chr11:57411380-57411530	HMF	breast:	n/a	n/a
19	CTCF	chr11:57411440-57411590	SK-N-SH_RA	brain:	n/a	n/a
20	CTCF	chr11:57411380-57411530	RPTEC	kidney:	n/a	n/a
21	CTCF	chr11:57411380-57411530	K562	blood:	n/a	n/a
22	POLR2A	chr11:57404802-57417187	SK-N-MC	brain:	n/a	n/a
23	CTCF	chr11:57411380-57411530	HCT-116	colon:	n/a	n/a
24	CTCF	chr11:57411440-57411590	AoAF	blood vessel:	n/a	n/a
25	CTCF	chr11:57411420-57411570	HRE	kidney:	n/a	n/a
26	CTCF	chr11:57411460-57411610	NHDF-neo	bronchial:	n/a	n/a
27	CTCF	chr11:57411420-57411570	HUVEC	blood vessel:	n/a	n/a
28	CTCF	chr11:57411436-57411589	HUVEC	blood vessel:	n/a	n/a
29	CTCF	chr11:57411380-57411530	AG10803	skin:	n/a	n/a
30	CTCF	chr11:57411440-57411590	WI-38	lung:	n/a	n/a
31	CTCF	chr11:57411400-57411550	AG09319	gingival:	n/a	n/a
32	CTCF	chr11:57411460-57411610	A549	lung:	n/a	n/a
33	CTCF	chr11:57411420-57411570	HFF-Myc	foreskin:	n/a	n/a
34	CTCF	chr11:57411440-57411590	HPF	lung:	n/a	n/a
35	CTCF	chr11:57411487-57411607	Lung_OC	lung:	n/a	n/a
36	CTCF	chr11:57411418-57411562	Hela-S3	cervix:	n/a	n/a
37	MAX	chr11:57411376-57411669	MCF-7	breast:	n/a	chr11:57411540-57411550
38	CTCF	chr11:57411471-57411527	K562	blood:	n/a	n/a
39	CTCF	chr11:57411380-57411530	HPAF	blood vessel:	n/a	n/a
40	CTCF	chr11:57411460-57411610	HMF	breast:	n/a	n/a
41	CTCF	chr11:57411440-57411590	HCFaa	heart:	n/a	n/a
42	POLR2A	chr11:57411259-57411727	HUVEC	blood vessel:	n/a	n/a
43	CTCF	chr11:57411440-57411590	AG04450	lung:	n/a	n/a
44	CTCF	chr11:57411460-57411610	AG04450	lung:	n/a	n/a
45	POLR2A	chr11:57410100-57417938	PBDE	blood:	n/a	n/a
46	CTCF	chr11:57411400-57411550	Hela-S3	cervix:	n/a	n/a
47	MYC	chr11:57411360-57411675	K562	blood:	n/a	chr11:57411540-57411550
48	POLR2A	chr11:57411264-57411579	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr11:57411400-57411550	HCPEpiC	choroid plexus:	n/a	n/a
50	CTCF	chr11:57411380-57411530	WERI-Rb-1	eye:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57334278..57336865-chr11:57411196..57413730,2	K562	blood:
2	chr11:57334539..57338384-chr11:57406664..57411574,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000254602	TF binding region
CLP1	TF binding region
ENSG00000156587	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10792110	1.00[JPT][hapmap]
rs10896644	1.00[JPT][hapmap]
rs10896649	1.00[JPT][hapmap]
rs11229109	1.00[JPT][hapmap]
rs11570176	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs11570181	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1613592	0.84[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1631684	0.81[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1647394	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1647403	0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17455422	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1783826	0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1783827	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783829	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1783978	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1783979	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1783980	1.00[JPT][hapmap]
rs1783981	1.00[JPT][hapmap]
rs1783983	0.84[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1783984	0.88[AMR][1000 genomes]
rs1783985	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1785498	1.00[JPT][hapmap]
rs1798172	0.84[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1798173	0.81[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1798177	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2156638	1.00[JPT][hapmap]
rs2956981	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs3017889	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs36036499	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4611222	1.00[JPT][hapmap]
rs627145	1.00[JPT][hapmap]
rs653889	1.00[JPT][hapmap]
rs665058	1.00[JPT][hapmap]
rs7117020	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs7120868	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs7947357	1.00[CEU][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs929934	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers 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	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS 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	87 gene(s)	inside rSNPs	diseases
7	esv992553	chr11:57408294-57419351	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1783828	CD5	cis	parietal	SCAN
rs1783828	TIMM10	cis	parietal	SCAN
rs1783828	VWCE	cis	cerebellum	SCAN
rs1783828	MS4A7	cis	parietal	SCAN
rs1783828	YPEL4	cis	lung	GTEx
rs1783828	YPEL4	cis	lymphoblastoid	seeQTL
rs1783828	TNKS1BP1	cis	parietal	SCAN
rs1783828	TIMM10	cis	Esophagus Mucosa	GTEx
rs1783828	SLC43A3	cis	cerebellum	SCAN
rs1783828	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs1783828	OR5B17	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57403000-57412200	Weak transcription	Hela-S3	cervix
2	chr11:57407200-57412200	Weak transcription	Ovary	ovary
3	chr11:57407400-57412600	Weak transcription	GM12878-XiMat	blood
4	chr11:57407600-57412200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr11:57407600-57412200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr11:57407600-57412200	Weak transcription	Spleen	Spleen
7	chr11:57407600-57413000	Weak transcription	Right Ventricle	heart
8	chr11:57407600-57413200	Weak transcription	Esophagus	oesophagus
9	chr11:57407800-57412200	Weak transcription	Pancreas	Pancrea
10	chr11:57408000-57412000	Weak transcription	Colon Smooth Muscle	Colon
11	chr11:57408000-57412200	Weak transcription	Lung	lung
12	chr11:57408200-57412000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:57408200-57412000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:57408400-57412200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:57408800-57411600	Genic enhancers	H1 Cell Line	embryonic stem cell
16	chr11:57408800-57411800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr11:57408800-57412000	Weak transcription	Left Ventricle	heart
18	chr11:57408800-57412000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr11:57408800-57412000	Weak transcription	Right Atrium	heart
20	chr11:57408800-57412200	Weak transcription	Adipose Nuclei	Adipose
21	chr11:57408800-57412200	Weak transcription	Brain Hippocampus Middle	brain
22	chr11:57408800-57412200	Weak transcription	Thymus	Thymus
23	chr11:57408800-57412600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr11:57408800-57412600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:57408800-57413400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr11:57409000-57411600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
27	chr11:57409000-57411600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr11:57409000-57412000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr11:57409000-57412000	Weak transcription	Brain Angular Gyrus	brain
30	chr11:57409000-57412000	Weak transcription	Brain Anterior Caudate	brain
31	chr11:57409000-57412000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:57409000-57412000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr11:57409000-57412200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr11:57409000-57412200	Weak transcription	Brain Substantia Nigra	brain
35	chr11:57409000-57412200	Weak transcription	Fetal Intestine Small	intestine
36	chr11:57409000-57412200	Weak transcription	Fetal Kidney	kidney
37	chr11:57409000-57412200	Weak transcription	A549	lung
38	chr11:57409000-57412200	Weak transcription	HSMMtube	muscle
39	chr11:57409000-57413200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr11:57409000-57414400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:57409000-57416200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr11:57409200-57412000	Weak transcription	Fetal Brain Male	brain
43	chr11:57409200-57412200	Weak transcription	Liver	Liver
44	chr11:57409200-57412200	Weak transcription	HepG2	liver
45	chr11:57409200-57412200	Weak transcription	Osteobl	bone
46	chr11:57409200-57413600	Weak transcription	Primary T cells from cord blood	blood
47	chr11:57409400-57411600	Genic enhancers	HUES64 Cell Line	embryonic stem cell
48	chr11:57409400-57411800	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr11:57409400-57413000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr11:57409600-57411600	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links