Variant report

Variant	rs2282530
Chromosome Location	chr11:66177952-66177953
allele	A/G
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	POLR2A	chr11:66177546-66178943	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr11:66177940-66178113	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:66177886-66178189	K562	blood:	n/a	n/a
4	POLR2A	chr11:66176225-66178093	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:66175946..66178663-chr11:66245836..66248085,2	MCF-7	breast:
2	chr11:66139168..66140849-chr11:66177644..66179339,2	K562	blood:
3	chr11:66177353..66178934-chr11:66186708..66188933,2	K562	blood:

Variant related genes	Relation type
ENSG00000254510	TF binding region
ENSG00000174669	Chromatin interaction
ENSG00000174576	Chromatin interaction
ENSG00000254986	Chromatin interaction
ENSG00000255517	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1039594	0.88[EUR][1000 genomes]
rs1047029	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10750784	0.96[CEU][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs10791869	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10791872	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10791874	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10791876	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10896111	0.83[ASW][hapmap];0.96[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10896112	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10896115	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10896116	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227465	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11601396	0.88[EUR][1000 genomes]
rs11823140	0.92[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs12416747	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12576299	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12577196	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12577917	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs12785321	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12785651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12786563	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12794121	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1546358	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1784029	0.87[CEU][hapmap]
rs1785633	0.96[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs1785639	0.92[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs1892940	0.96[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs2236679	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2279861	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2279862	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2282531	0.96[CEU][hapmap]
rs3016767	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3177514	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34043951	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4244813	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4466842	0.92[CEU][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4930177	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4930178	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4930179	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4930181	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930360	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4930362	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4930363	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930366	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930368	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55998145	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56123976	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56321771	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61891449	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6591213	0.96[CEU][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6591215	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6591217	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66810040	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7104253	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7104570	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7105015	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7105401	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7107191	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7110944	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7117630	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7126018	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73489638	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7938676	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7939111	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7940980	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs905770	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs947978	0.96[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
2	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
3	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv832193	chr11:66120339-66278805	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2282530	ALDH3B1	cis	parietal	SCAN
rs2282530	SLC25A45	cis	parietal	SCAN
rs2282530	SCYL1	cis	lymphoblastoid	seeQTL
rs2282530	ASRGL1	cis	parietal	SCAN
rs2282530	B3GNT1	cis	parietal	SCAN
rs2282530	OVOL1	cis	parietal	SCAN
rs2282530	RIN1	cis	Whole Blood	GTEx
rs2282530	ACTN3	cis	lymphoblastoid	seeQTL
rs2282530	ESRRA	cis	cerebellum	SCAN
rs2282530	MACROD1	cis	parietal	SCAN
rs2282530	RP11-867G23.12	cis	Whole Blood	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66176200-66178200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
2	chr11:66176600-66179800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr11:66176800-66178400	Flanking Active TSS	Rectal Smooth Muscle	rectum
4	chr11:66176800-66178400	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr11:66176800-66178600	Weak transcription	Aorta	Aorta
6	chr11:66177000-66178000	Weak transcription	Ovary	ovary
7	chr11:66177000-66179400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:66177000-66179400	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr11:66177000-66180200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr11:66177000-66180600	Weak transcription	Fetal Brain Male	brain
11	chr11:66177000-66181000	Weak transcription	Spleen	Spleen
12	chr11:66177000-66181800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:66177000-66183600	Weak transcription	Right Atrium	heart
14	chr11:66177200-66179200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:66177200-66179600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:66177200-66180000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr11:66177200-66180000	Active TSS	Colon Smooth Muscle	Colon
18	chr11:66177200-66180600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:66177400-66178600	Active TSS	Brain Germinal Matrix	brain
20	chr11:66177400-66180800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:66177400-66181000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr11:66177400-66185000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:66177600-66178000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr11:66177600-66178000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr11:66177600-66178200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr11:66177600-66180400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr11:66177600-66181400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:66177600-66184600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:66177800-66178000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr11:66177800-66178000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr11:66177800-66178000	Enhancers	Fetal Heart	heart
32	chr11:66177800-66178200	Bivalent/Poised TSS	Fetal Stomach	stomach
33	chr11:66177800-66178800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links