Variant report

Variant	rs6486209
Chromosome Location	chr11:9230454-9230455
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	MTA3	chr11:9230231-9231467	GM12878	blood:	n/a	n/a
5	RELA	chr11:9230384-9231019	GM19099	blood:	n/a	n/a
6	POLR2A	chr11:9230221-9231245	GM12892	blood:	n/a	n/a
7	RELA	chr11:9230376-9230913	GM19193	blood:	n/a	n/a
8	RUNX3	chr11:9230168-9231582	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:9230310-9231263	GM12878	blood:	n/a	n/a
10	BCL11A	chr11:9230392-9230773	GM12878	blood:	n/a	n/a
11	FOXM1	chr11:9230377-9231364	GM12878	blood:	n/a	n/a
12	MTA3	chr11:9230249-9231272	GM12878	blood:	n/a	n/a
13	YY1	chr11:9230377-9231102	GM12878	blood:	n/a	n/a
14	NFATC1	chr11:9230265-9231004	GM12878	blood:	n/a	n/a
15	PML	chr11:9230173-9231425	GM12878	blood:	n/a	n/a
16	RELA	chr11:9230324-9231483	GM12878	blood:	n/a	n/a
17	RUNX3	chr11:9230333-9231523	GM12878	blood:	n/a	n/a
18	STAT5A	chr11:9230390-9231502	GM12878	blood:	n/a	n/a
19	ATF2	chr11:9230296-9231444	GM12878	blood:	n/a	n/a
20	TEAD4	chr11:9230421-9231090	K562	blood:	n/a	n/a
21	STAT5A	chr11:9230376-9231354	GM12878	blood:	n/a	n/a
22	BATF	chr11:9230376-9231506	GM12878	blood:	n/a	n/a
23	YY1	chr11:9230337-9230540	GM12878	blood:	n/a	n/a
24	POLR2A	chr11:9230358-9231039	GM12892	blood:	n/a	n/a
25	POLR2A	chr11:9230304-9230759	GM12891	blood:	n/a	n/a
26	TCF12	chr11:9230332-9230592	GM12878	blood:	n/a	n/a
27	BCL3	chr11:9230321-9230845	GM12878	blood:	n/a	n/a
28	NFIC	chr11:9230034-9233381	GM12878	blood:	n/a	n/a
29	NFIC	chr11:9230313-9231457	GM12878	blood:	n/a	n/a
30	POLR2A	chr11:9230199-9231110	GM12892	blood:	n/a	n/a
31	CEBPB	chr11:9230389-9230676	GM12878	blood:	n/a	n/a
32	FOXM1	chr11:9230170-9231524	GM12878	blood:	n/a	n/a
33	BCLAF1	chr11:9229999-9230987	GM12878	blood:	n/a	n/a
34	RELA	chr11:9230338-9231543	GM12891	blood:	n/a	n/a
35	IKZF1	chr11:9230406-9231363	GM12878	blood:	n/a	n/a
36	MEF2A	chr11:9230263-9230847	GM12878	blood:	n/a	chr11:9230564-9230579 chr11:9230282-9230290 chr11:9230566-9230581 chr11:9230564-9230579
37	MEF2C	chr11:9230354-9231082	GM12878	blood:	n/a	chr11:9230564-9230579 chr11:9230995-9231010 chr11:9230566-9230581 chr11:9230564-9230579
38	ATF2	chr11:9230249-9231465	GM12878	blood:	n/a	n/a
39	PAX5	chr11:9230393-9231054	GM12878	blood:	n/a	n/a

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: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10454487	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840186	0.82[EUR][1000 genomes]
rs10840188	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840189	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042179	0.81[AMR][1000 genomes]
rs11042190	0.83[AMR][1000 genomes]
rs11042191	0.83[AMR][1000 genomes]
rs11042192	0.83[AMR][1000 genomes]
rs11042197	0.89[AMR][1000 genomes]
rs11042215	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042217	1.00[ASN][1000 genomes]
rs11042224	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042228	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042230	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042231	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042232	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042233	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042240	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042241	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042242	1.00[ASN][1000 genomes]
rs11042246	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042253	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042257	0.87[EUR][1000 genomes]
rs11042259	0.87[EUR][1000 genomes]
rs11042268	0.83[EUR][1000 genomes]
rs11827186	0.81[EUR][1000 genomes]
rs12286621	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360767	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12362997	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12363839	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366113	0.83[AMR][1000 genomes]
rs17257379	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133215	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4627079	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4910446	0.87[EUR][1000 genomes]
rs4910447	0.81[EUR][1000 genomes]
rs55962227	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56294473	1.00[ASN][1000 genomes]
rs60693427	1.00[ASN][1000 genomes]
rs6486204	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66554737	1.00[ASN][1000 genomes]
rs7103472	0.83[EUR][1000 genomes]
rs7115283	0.88[EUR][1000 genomes]
rs7115373	0.83[EUR][1000 genomes]
rs7121753	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129049	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130400	1.00[ASN][1000 genomes]
rs72850512	0.83[EUR][1000 genomes]
rs72857989	0.85[AMR][1000 genomes]
rs72857991	0.89[AMR][1000 genomes]
rs72857993	0.89[AMR][1000 genomes]
rs72857997	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72859608	0.88[EUR][1000 genomes]
rs72859676	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72859678	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72859693	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72861335	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72861360	0.81[EUR][1000 genomes]
rs7394454	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7394869	1.00[ASN][1000 genomes]
rs7395631	1.00[ASN][1000 genomes]
rs7396130	0.89[AMR][1000 genomes]
rs7396541	0.89[AMR][1000 genomes]
rs7929621	1.00[ASN][1000 genomes]
rs7936622	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938562	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7939704	0.81[EUR][1000 genomes]
rs7940872	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945570	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945759	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7949349	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9645644	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9162000-9230600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:9169600-9238000	Weak transcription	Esophagus	oesophagus
3	chr11:9182400-9231800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr11:9201000-9230800	Weak transcription	HMEC	breast
5	chr11:9202600-9251200	Weak transcription	Small Intestine	intestine
6	chr11:9223600-9230800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:9224000-9232600	Weak transcription	Colonic Mucosa	Colon
8	chr11:9225400-9236800	Weak transcription	Primary B cells from cord blood	blood
9	chr11:9225600-9230800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr11:9225600-9232400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr11:9225800-9230600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr11:9225800-9230600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:9225800-9230800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:9225800-9231200	Weak transcription	NHEK	skin
15	chr11:9225800-9232000	Weak transcription	Spleen	Spleen
16	chr11:9225800-9234400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr11:9225800-9236200	Weak transcription	Thymus	Thymus
18	chr11:9225800-9237800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:9225800-9237800	Weak transcription	Gastric	stomach
20	chr11:9226000-9230800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:9226000-9232000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:9226000-9236400	Weak transcription	Lung	lung
23	chr11:9226000-9236800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr11:9226000-9241200	Weak transcription	Aorta	Aorta
25	chr11:9226000-9252000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:9226000-9252800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr11:9226200-9236200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:9226600-9230600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr11:9226800-9230800	Weak transcription	Hela-S3	cervix
30	chr11:9227200-9236600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr11:9227400-9230600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:9227400-9236200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:9227400-9236400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:9227400-9250400	Weak transcription	Fetal Stomach	stomach
35	chr11:9227600-9230800	Weak transcription	Fetal Muscle Leg	muscle
36	chr11:9227600-9236400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr11:9227600-9250600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr11:9227800-9230600	Weak transcription	Placenta	Placenta
39	chr11:9228000-9232600	Enhancers	Brain Cingulate Gyrus	brain
40	chr11:9228200-9231200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:9228400-9232000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr11:9228400-9232400	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr11:9228400-9232600	Enhancers	Brain Substantia Nigra	brain
44	chr11:9228400-9232800	Enhancers	Brain Anterior Caudate	brain
45	chr11:9228400-9236400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr11:9228400-9236600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr11:9228400-9236600	Weak transcription	HUVEC	blood vessel
48	chr11:9228600-9232000	Weak transcription	HepG2	liver
49	chr11:9228600-9232200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:9228600-9232800	Enhancers	Brain Hippocampus Middle	brain

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