Variant report

Variant	rs11593876
Chromosome Location	chr10:5857001-5857002
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:5854614-5857010	GM19193	blood:	n/a	n/a
2	MXI1	chr10:5852991-5857043	SK-N-SH	brain:	n/a	chr10:5855794-5855803 chr10:5855794-5855803 chr10:5855796-5855805
3	POLR2A	chr10:5856731-5857043	K562	blood:	n/a	n/a
4	POLR2A	chr10:5856529-5857045	GM12891	blood:	n/a	n/a
5	POLR2A	chr10:5852865-5857536	MCF10A-Er-Src	breast:	n/a	n/a
6	ESRRA	chr10:5853937-5857177	GM12878	blood:	n/a	chr10:5855737-5855749 chr10:5854470-5854482 chr10:5854465-5854481
7	POLR2A	chr10:5854618-5857409	GM18951	blood:	n/a	n/a
8	POLR2A	chr10:5853823-5857228	GM12878	blood:	n/a	n/a
9	POLR2A	chr10:5854191-5857525	GM12892	blood:	n/a	n/a
10	POLR2A	chr10:5854313-5857041	GM12892	blood:	n/a	n/a
11	POLR2A	chr10:5856519-5857149	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr10:5854147-5859027	GM12891	blood:	n/a	n/a
13	POLR2A	chr10:5856766-5857361	GM12891	blood:	n/a	n/a
14	POLR2A	chr10:5855185-5857664	K562	blood:	n/a	n/a
15	POLR2A	chr10:5854582-5857443	K562	blood:	n/a	n/a
16	POLR2A	chr10:5854697-5857370	K562	blood:	n/a	n/a
17	POLR2A	chr10:5856741-5857466	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr10:5856695-5857047	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr10:5854387-5857333	K562	blood:	n/a	n/a
20	POLR2A	chr10:5854182-5857522	GM12878	blood:	n/a	n/a
21	POLR2A	chr10:5854462-5858661	Raji	blood:	n/a	n/a
22	POLR2A	chr10:5856951-5857469	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr10:5854799-5857185	NB4	blood:	n/a	n/a
24	POLR2A	chr10:5856624-5857691	HepG2	liver:	n/a	n/a
25	POLR2A	chr10:5854306-5857324	GM19099	blood:	n/a	n/a
26	POLR2A	chr10:5854416-5857032	K562	blood:	n/a	n/a
27	POLR2A	chr10:5856754-5857691	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr10:5854182-5857602	GM12878	blood:	n/a	n/a
29	POLR2A	chr10:5856655-5857570	GM12878	blood:	n/a	n/a
30	MXI1	chr10:5854360-5857069	IMR90	lung:	n/a	chr10:5855794-5855803 chr10:5855794-5855803 chr10:5855796-5855805
31	POLR2A	chr10:5854462-5857077	MCF-7	breast:	n/a	n/a
32	POLR2A	chr10:5854209-5857035	K562	blood:	n/a	n/a
33	POLR2A	chr10:5854215-5857590	GM12892	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5725503..5729426-chr10:5853777..5860412,5	MCF-7	breast:
2	chr10:5853439..5857708-chr10:5926443..5936823,24	K562	blood:
3	chr10:5852473..5857853-chr10:5880942..5888645,8	MCF-7	breast:
4	chr10:5853575..5857221-chr10:5900529..5905112,5	MCF-7	breast:
5	chr10:5732056..5734929-chr10:5855542..5857938,2	K562	blood:
6	chr10:5664947..5667027-chr10:5854331..5857046,2	MCF-7	breast:
7	chr10:5851570..5858995-chr10:5881654..5887342,9	K562	blood:
8	chr10:5855633..5857899-chr8:144821553..144823070,2	MCF-7	breast:
9	chr10:5815026..5819070-chr10:5852954..5857275,5	MCF-7	breast:
10	chr10:5725239..5729489-chr10:5854026..5858186,8	K562	blood:
11	chr10:5852595..5861125-chr10:5921136..5936216,31	MCF-7	breast:
12	chr10:5809711..5811648-chr10:5855446..5857250,2	K562	blood:
13	chr10:5810148..5812616-chr10:5855203..5857512,4	K562	blood:
14	chr10:5853532..5857435-chr10:5928623..5934190,13	MCF-7	breast:

No data

Variant related genes	Relation type
GDI2	TF binding region
ENSG00000203499	Chromatin interaction
ENSG00000240180	Chromatin interaction
ENSG00000134452	Chromatin interaction
ENSG00000108021	Chromatin interaction
ENSG00000270427	Chromatin interaction
ENSG00000057608	Chromatin interaction
ENSG00000228685	Chromatin interaction
ENSG00000134461	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1057943	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11592993	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11594505	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11594846	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11595421	0.96[EUR][1000 genomes]
rs11596702	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11599810	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386620	0.83[EUR][1000 genomes]
rs2386664	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2797484	0.81[EUR][1000 genomes]
rs3736460	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45549643	0.96[EUR][1000 genomes]
rs59758327	0.91[EUR][1000 genomes]
rs61832759	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61832860	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61832863	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61832864	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61832865	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61832866	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61832870	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61832872	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61832874	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61832878	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61836362	0.82[EUR][1000 genomes]
rs7076584	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7093027	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72772369	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72774084	0.97[EUR][1000 genomes]
rs7475869	0.95[EUR][1000 genomes]
rs7902987	0.87[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	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer 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	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv515935	chr10:5820394-5869839	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv549896	chr10:5820394-5880066	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5856000-5857200	Flanking Active TSS	Dnd41	blood
2	chr10:5856000-5857400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr10:5856000-5857400	Flanking Active TSS	GM12878-XiMat	blood
4	chr10:5856200-5857200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr10:5856200-5857400	Enhancers	Spleen	Spleen
6	chr10:5856200-5862600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:5856400-5857200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr10:5856400-5857200	Enhancers	Colon Smooth Muscle	Colon
9	chr10:5856400-5857400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr10:5856400-5857400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr10:5856400-5857400	Enhancers	Fetal Intestine Large	intestine
12	chr10:5856400-5857400	Enhancers	Fetal Intestine Small	intestine
13	chr10:5856400-5857400	Enhancers	Pancreas	Pancrea
14	chr10:5856400-5858400	Weak transcription	HSMM	muscle
15	chr10:5856400-5859000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:5856400-5859800	Weak transcription	Esophagus	oesophagus
17	chr10:5856600-5857200	Enhancers	Liver	Liver
18	chr10:5856600-5857200	Enhancers	Fetal Kidney	kidney
19	chr10:5856600-5857200	Enhancers	Stomach Mucosa	stomach
20	chr10:5856600-5857400	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr10:5856600-5857400	Enhancers	Primary hematopoietic stem cells	blood
22	chr10:5856600-5857400	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr10:5856600-5857400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr10:5856600-5857400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr10:5856600-5857400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr10:5856600-5857400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr10:5856600-5857400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr10:5856600-5857400	Enhancers	Fetal Muscle Leg	muscle
29	chr10:5856600-5857400	Enhancers	Fetal Thymus	thymus
30	chr10:5856600-5857400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr10:5856600-5857400	Enhancers	Rectal Smooth Muscle	rectum
32	chr10:5856600-5857400	Enhancers	HepG2	liver
33	chr10:5856600-5857800	Enhancers	Primary T cells fromperipheralblood	blood
34	chr10:5856600-5858600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr10:5856600-5861600	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr10:5856800-5857200	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr10:5856800-5857200	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr10:5856800-5857200	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr10:5856800-5857200	Enhancers	Duodenum Mucosa	Duodenum
40	chr10:5856800-5857200	Enhancers	Fetal Heart	heart
41	chr10:5856800-5857200	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr10:5856800-5857400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr10:5856800-5857400	Enhancers	Primary T cells from cord blood	blood
44	chr10:5856800-5857400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr10:5856800-5857400	Enhancers	Brain Germinal Matrix	brain
46	chr10:5856800-5857400	Enhancers	Fetal Lung	lung
47	chr10:5856800-5857400	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr10:5856800-5857400	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr10:5856800-5857400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr10:5856800-5857400	Genic enhancers	K562	blood

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