Variant report

Variant	rs1544863
Chromosome Location	chr11:10676255-10676256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr11:10675687-10677428	HCT-116	colon:	n/a	n/a
2	RAD21	chr11:10675782-10676350	A549	lung:	n/a	chr11:10676007-10676026
3	RAD21	chr11:10675727-10676256	HepG2	liver:	n/a	chr11:10676007-10676026
4	RAD21	chr11:10675506-10676419	SK-N-SH	brain:	n/a	chr11:10676007-10676026 chr11:10676363-10676370
5	CTCF	chr11:10675307-10676475	A549	lung:	n/a	chr11:10676010-10676026 chr11:10676009-10676027 chr11:10676004-10676025
6	CTCF	chr11:10675547-10676820	SK-N-SH	brain:	n/a	chr11:10676010-10676026 chr11:10676009-10676027 chr11:10676004-10676025
7	SMC3	chr11:10675705-10676260	GM12878	blood:	n/a	chr11:10676011-10676025
8	EP300	chr11:10675862-10676260	K562	blood:	n/a	n/a
9	MAFF	chr11:10675898-10676390	K562	blood:	n/a	n/a
10	RAD21	chr11:10675763-10676275	ECC-1	luminal epithelium:	n/a	chr11:10676007-10676026
11	RAD21	chr11:10675659-10676300	MCF-7	breast:	n/a	chr11:10676007-10676026
12	RAD21	chr11:10675590-10676423	HCT-116	colon:	n/a	chr11:10676007-10676026 chr11:10676363-10676370
13	CTCF	chr11:10675766-10676322	K562	blood:	n/a	chr11:10676010-10676026 chr11:10676009-10676027 chr11:10676004-10676025
14	RAD21	chr11:10675532-10677194	HCT-116	colon:	n/a	chr11:10676007-10676026 chr11:10676363-10676370
15	CTCF	chr11:10675640-10676680	HCT-116	colon:	n/a	chr11:10676010-10676026 chr11:10676009-10676027 chr11:10676004-10676025
16	SMC3	chr11:10675423-10676487	SK-N-SH	brain:	n/a	chr11:10676011-10676025
17	RAD21	chr11:10675674-10676299	ECC-1	luminal epithelium:	n/a	chr11:10676007-10676026
18	CTCF	chr11:10675721-10676291	K562	blood:	n/a	chr11:10676010-10676026 chr11:10676009-10676027 chr11:10676004-10676025
19	WRNIP1	chr11:10675807-10676421	GM12878	blood:	n/a	n/a
20	SP1	chr11:10675697-10677347	HCT-116	colon:	n/a	n/a
21	CTCF	chr11:10676240-10676390	AoAF	blood vessel:	n/a	n/a
22	CTCF	chr11:10676240-10676390	HRPEpiC	eye:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:10584920..10587068-chr11:10674559..10677361,2	K562	blood:
2	chr11:10535798..10536641-chr11:10675860..10676528,2	K562	blood:
3	chr11:10427811..10428324-chr11:10675560..10676361,2	MCF-7	breast:
4	chr11:10427762..10428619-chr11:10675503..10676394,3	K562	blood:
5	chr11:10675148..10677906-chr11:10678421..10681418,4	MCF-7	breast:
6	chr11:10675809..10676339-chr11:10757361..10757900,2	MCF-7	breast:
7	chr11:10535531..10536556-chr11:10675584..10676325,3	MCF-7	breast:
8	chr11:10322610..10325546-chr11:10673380..10676333,2	K562	blood:
9	chr11:10562743..10563281-chr11:10675875..10676455,2	K562	blood:
10	chr11:10534042..10535923-chr11:10675097..10677538,2	MCF-7	breast:
11	chr11:10560102..10563921-chr11:10672313..10677222,4	MCF-7	breast:
12	chr11:10674925..10678334-chr11:10679453..10682484,4	MCF-7	breast:
13	chr11:10646146..10646679-chr11:10675883..10676500,2	MCF-7	breast:
14	chr11:10675716..10676486-chr11:10756936..10757598,2	K562	blood:
15	chr11:10645746..10646712-chr11:10675224..10676417,4	K562	blood:

Variant related genes	Relation type
MRVI1	TF binding region
ENSG00000254554	Chromatin interaction
ENSG00000110315	Chromatin interaction
ENSG00000177112	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10770129	0.81[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10770130	0.96[ASN][1000 genomes]
rs10770132	0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs10770133	0.85[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs10840456	0.81[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10840458	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840459	0.89[ASN][1000 genomes]
rs10840460	0.94[ASN][1000 genomes]
rs10840461	0.94[ASN][1000 genomes]
rs10840462	0.94[ASN][1000 genomes]
rs10840463	0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10840464	0.94[ASN][1000 genomes]
rs10840465	0.94[ASN][1000 genomes]
rs10840466	0.94[ASN][1000 genomes]
rs10840467	0.93[ASN][1000 genomes]
rs10840468	0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs11042910	0.90[JPT][hapmap]
rs11042911	0.86[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs11042913	0.94[ASN][1000 genomes]
rs12295574	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12363422	0.85[ASN][1000 genomes]
rs12420672	0.85[ASN][1000 genomes]
rs12420675	0.85[ASN][1000 genomes]
rs1390572	0.94[ASN][1000 genomes]
rs1390573	0.87[ASN][1000 genomes]
rs1425149	0.94[ASN][1000 genomes]
rs1425150	0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1425151	0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1544862	0.94[ASN][1000 genomes]
rs1559652	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16908157	0.85[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs16908159	0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs16908162	0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1845832	0.94[ASN][1000 genomes]
rs1874444	0.94[ASN][1000 genomes]
rs1895712	0.94[ASN][1000 genomes]
rs2098840	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2113897	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34554801	0.89[ASN][1000 genomes]
rs35040034	0.94[ASN][1000 genomes]
rs35165550	0.85[ASN][1000 genomes]
rs3993279	0.91[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4243916	0.87[ASN][1000 genomes]
rs4909943	0.91[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4909944	0.91[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4909946	0.87[ASN][1000 genomes]
rs4910166	0.85[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs722274	0.94[ASN][1000 genomes]
rs745336	0.87[ASN][1000 genomes]
rs750540	0.85[ASN][1000 genomes]
rs7925193	0.84[JPT][hapmap]
rs7933525	0.94[ASN][1000 genomes]
rs7935285	0.83[JPT][hapmap]
rs7938027	0.87[ASN][1000 genomes]
rs7938635	0.84[JPT][hapmap]
rs7939662	0.85[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7939686	0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs881870	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs903825	0.85[ASN][1000 genomes]
rs903826	0.85[ASN][1000 genomes]
rs903827	0.85[ASN][1000 genomes]
rs903828	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv832063	chr11:10618485-10785281	ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1544863	GVIN1	cis	cerebellum	SCAN
rs1544863	RRAS2	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10646000-10679000	Weak transcription	Fetal Lung	lung
2	chr11:10646200-10679200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr11:10650400-10678600	Weak transcription	Right Ventricle	heart
4	chr11:10658800-10676600	Enhancers	Primary B cells from peripheral blood	blood
5	chr11:10664200-10678800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:10669600-10676800	Weak transcription	Fetal Intestine Large	intestine
7	chr11:10670800-10676400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:10671400-10677000	Weak transcription	Fetal Intestine Small	intestine
9	chr11:10672000-10679200	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr11:10673000-10682200	Enhancers	Placenta	Placenta
11	chr11:10673200-10676800	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr11:10673200-10677800	Enhancers	Colon Smooth Muscle	Colon
13	chr11:10673400-10676600	Enhancers	Spleen	Spleen
14	chr11:10673400-10679200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr11:10673400-10682800	Enhancers	Ovary	ovary
16	chr11:10673600-10678400	Weak transcription	Left Ventricle	heart
17	chr11:10673600-10678400	Weak transcription	Right Atrium	heart
18	chr11:10673800-10678800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:10673800-10679200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr11:10673800-10681400	Weak transcription	Pancreas	Pancrea
21	chr11:10674000-10676400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:10674000-10676600	Weak transcription	NH-A	brain
23	chr11:10674000-10677200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr11:10674000-10677400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:10674000-10681400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr11:10674200-10676600	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr11:10674200-10681800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr11:10674400-10678000	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr11:10674400-10681400	Enhancers	Fetal Muscle Leg	muscle
30	chr11:10674400-10681800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr11:10674600-10678400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:10674600-10678400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr11:10674600-10689600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr11:10674800-10677000	Weak transcription	Colonic Mucosa	Colon
35	chr11:10674800-10678800	Enhancers	Rectal Smooth Muscle	rectum
36	chr11:10675000-10676400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr11:10675000-10678800	Enhancers	K562	blood
38	chr11:10675200-10676400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr11:10675200-10676800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr11:10675200-10677600	Enhancers	Primary B cells from cord blood	blood
41	chr11:10675200-10677800	Enhancers	Stomach Smooth Muscle	stomach
42	chr11:10675200-10679000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:10675400-10676400	Strong transcription	Fetal Stomach	stomach
44	chr11:10675400-10678600	Enhancers	GM12878-XiMat	blood
45	chr11:10675400-10678800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr11:10675600-10677200	Enhancers	HMEC	breast
47	chr11:10675600-10677400	Genic enhancers	Aorta	Aorta
48	chr11:10675600-10677400	Weak transcription	Fetal Thymus	thymus
49	chr11:10675600-10677400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr11:10675600-10677600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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