Variant report

Variant	rs6486210
Chromosome Location	chr11:9230738-9230739
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	MEF2A	chr11:9230340-9230911	GM12878	blood:	n/a	chr11:9230564-9230579 chr11:9230566-9230581 chr11:9230564-9230579
2	POLR2A	chr11:9230344-9230889	GM12891	blood:	n/a	n/a
3	RELA	chr11:9230339-9231388	GM18951	blood:	n/a	n/a
4	YY1	chr11:9230650-9230976	K562	blood:	n/a	n/a
5	UBTF	chr11:9230634-9230798	K562	blood:	n/a	n/a
6	MTA3	chr11:9230231-9231467	GM12878	blood:	n/a	n/a
7	RELA	chr11:9230384-9231019	GM19099	blood:	n/a	n/a
8	POLR2A	chr11:9230221-9231245	GM12892	blood:	n/a	n/a
9	POLR2A	chr11:9230672-9231081	GM12891	blood:	n/a	n/a
10	BHLHE40	chr11:9230698-9230923	K562	blood:	n/a	n/a
11	WRNIP1	chr11:9230720-9231081	GM12878	blood:	n/a	n/a
12	RELA	chr11:9230376-9230913	GM19193	blood:	n/a	n/a
13	YY1	chr11:9230640-9230989	GM12878	blood:	n/a	n/a
14	RUNX3	chr11:9230168-9231582	GM12878	blood:	n/a	n/a
15	TEAD4	chr11:9230489-9230994	K562	blood:	n/a	n/a
16	POLR2A	chr11:9230310-9231263	GM12878	blood:	n/a	n/a
17	BCL11A	chr11:9230392-9230773	GM12878	blood:	n/a	n/a
18	FOXM1	chr11:9230377-9231364	GM12878	blood:	n/a	n/a
19	MTA3	chr11:9230249-9231272	GM12878	blood:	n/a	n/a
20	YY1	chr11:9230377-9231102	GM12878	blood:	n/a	n/a
21	JUND	chr11:9230508-9230997	K562	blood:	n/a	n/a
22	NFATC1	chr11:9230265-9231004	GM12878	blood:	n/a	n/a
23	PML	chr11:9230173-9231425	GM12878	blood:	n/a	n/a
24	RELA	chr11:9230324-9231483	GM12878	blood:	n/a	n/a
25	YY1	chr11:9230637-9230965	GM12891	blood:	n/a	n/a
26	RUNX3	chr11:9230333-9231523	GM12878	blood:	n/a	n/a
27	YY1	chr11:9230569-9231023	GM12892	blood:	n/a	n/a
28	STAT5A	chr11:9230390-9231502	GM12878	blood:	n/a	n/a
29	ATF2	chr11:9230296-9231444	GM12878	blood:	n/a	n/a
30	TEAD4	chr11:9230421-9231090	K562	blood:	n/a	n/a
31	CUX1	chr11:9230587-9230877	K562	blood:	n/a	n/a
32	IRF1	chr11:9230578-9230802	K562	blood:	n/a	chr11:9230627-9230641 chr11:9230630-9230642
33	STAT5A	chr11:9230376-9231354	GM12878	blood:	n/a	n/a
34	BATF	chr11:9230376-9231506	GM12878	blood:	n/a	n/a
35	POLR2A	chr11:9230358-9231039	GM12892	blood:	n/a	n/a
36	YY1	chr11:9230638-9231036	GM12878	blood:	n/a	n/a
37	POLR2A	chr11:9230304-9230759	GM12891	blood:	n/a	n/a
38	BCL3	chr11:9230321-9230845	GM12878	blood:	n/a	n/a
39	YY1	chr11:9230608-9230940	K562	blood:	n/a	n/a
40	STAT1	chr11:9230684-9230975	GM12878	blood:	n/a	n/a
41	NFIC	chr11:9230034-9233381	GM12878	blood:	n/a	n/a
42	NFIC	chr11:9230313-9231457	GM12878	blood:	n/a	n/a
43	POLR2A	chr11:9230199-9231110	GM12892	blood:	n/a	n/a
44	FOXM1	chr11:9230170-9231524	GM12878	blood:	n/a	n/a
45	BCLAF1	chr11:9229999-9230987	GM12878	blood:	n/a	n/a
46	YY1	chr11:9230562-9230999	GM12892	blood:	n/a	n/a
47	RELA	chr11:9230338-9231543	GM12891	blood:	n/a	n/a
48	RCOR1	chr11:9230671-9231086	K562	blood:	n/a	n/a
49	IKZF1	chr11:9230406-9231363	GM12878	blood:	n/a	n/a
50	MEF2A	chr11:9230263-9230847	GM12878	blood:	n/a	chr11:9230564-9230579 chr11:9230282-9230290 chr11:9230566-9230581 chr11:9230564-9230579

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9229489..9231111-chr11:9235259..9236872,2	K562	blood:

Variant related genes	Relation type
DENND5A	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10770000	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10770001	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10770002	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10770003	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10770004	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10770006	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap]
rs10770008	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap]
rs10770010	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap]
rs10770016	0.84[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs10840196	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11042182	0.80[TSI][hapmap]
rs11042200	0.95[YRI][hapmap]
rs11042227	0.93[ASN][1000 genomes]
rs11042245	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11042252	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11042267	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs11608172	0.93[ASN][1000 genomes]
rs12289113	0.93[ASN][1000 genomes]
rs12295767	0.90[ASN][1000 genomes]
rs12296016	0.94[ASN][1000 genomes]
rs12420463	0.88[ASN][1000 genomes]
rs12577661	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2133216	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2873069	0.92[ASN][1000 genomes]
rs34729888	0.93[ASN][1000 genomes]
rs35686957	0.80[EUR][1000 genomes]
rs35757766	0.88[ASN][1000 genomes]
rs35955530	0.93[ASN][1000 genomes]
rs4369406	0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap]
rs5014247	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs61877814	0.93[ASN][1000 genomes]
rs61877916	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6486206	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs6486215	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6486226	0.93[ASN][1000 genomes]
rs6486231	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7101432	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7104221	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs7109911	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7112540	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7114688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7115062	0.93[ASN][1000 genomes]
rs7116459	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs7121013	0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs7123342	0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs71476818	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7394878	0.95[YRI][hapmap]
rs7396439	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7482630	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs770	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7924664	0.93[ASN][1000 genomes]
rs7925308	0.95[YRI][hapmap]
rs7930507	0.95[YRI][hapmap]
rs7933448	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7941520	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs952374	0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs9736263	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9888193	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9888229	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040049	chr11:9152536-9363488	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1053045	chr11:9208881-9363488	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv540947	chr11:9208881-9363488	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6486210	MRPL17	cis	parietal	SCAN
rs6486210	CCKBR	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9169600-9238000	Weak transcription	Esophagus	oesophagus
2	chr11:9182400-9231800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr11:9201000-9230800	Weak transcription	HMEC	breast
4	chr11:9202600-9251200	Weak transcription	Small Intestine	intestine
5	chr11:9223600-9230800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:9224000-9232600	Weak transcription	Colonic Mucosa	Colon
7	chr11:9225400-9236800	Weak transcription	Primary B cells from cord blood	blood
8	chr11:9225600-9230800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr11:9225600-9232400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr11:9225800-9230800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:9225800-9231200	Weak transcription	NHEK	skin
12	chr11:9225800-9232000	Weak transcription	Spleen	Spleen
13	chr11:9225800-9234400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr11:9225800-9236200	Weak transcription	Thymus	Thymus
15	chr11:9225800-9237800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr11:9225800-9237800	Weak transcription	Gastric	stomach
17	chr11:9226000-9230800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:9226000-9232000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:9226000-9236400	Weak transcription	Lung	lung
20	chr11:9226000-9236800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr11:9226000-9241200	Weak transcription	Aorta	Aorta
22	chr11:9226000-9252000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr11:9226000-9252800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr11:9226200-9236200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:9226800-9230800	Weak transcription	Hela-S3	cervix
26	chr11:9227200-9236600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr11:9227400-9236200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr11:9227400-9236400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:9227400-9250400	Weak transcription	Fetal Stomach	stomach
30	chr11:9227600-9230800	Weak transcription	Fetal Muscle Leg	muscle
31	chr11:9227600-9236400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr11:9227600-9250600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr11:9228000-9232600	Enhancers	Brain Cingulate Gyrus	brain
34	chr11:9228200-9231200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr11:9228400-9232000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr11:9228400-9232400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr11:9228400-9232600	Enhancers	Brain Substantia Nigra	brain
38	chr11:9228400-9232800	Enhancers	Brain Anterior Caudate	brain
39	chr11:9228400-9236400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:9228400-9236600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr11:9228400-9236600	Weak transcription	HUVEC	blood vessel
42	chr11:9228600-9232000	Weak transcription	HepG2	liver
43	chr11:9228600-9232200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:9228600-9232800	Enhancers	Brain Hippocampus Middle	brain
45	chr11:9228800-9231400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr11:9228800-9232000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr11:9228800-9232400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr11:9228800-9232800	Enhancers	Fetal Heart	heart
49	chr11:9229000-9230800	Weak transcription	NH-A	brain
50	chr11:9229000-9231200	Enhancers	HSMM	muscle

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