Variant report

Variant	rs11011415
Chromosome Location	chr10:38264389-38264390
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	CEBPB	chr10:38264163-38264594	MCF-7	breast:	n/a	chr10:38264394-38264402
2	TBP	chr10:38264337-38265911	K562	blood:	n/a	n/a
3	CEBPB	chr10:38264214-38264546	IMR90	lung:	n/a	chr10:38264394-38264402
4	MYC	chr10:38264220-38266048	NB4	blood:	n/a	n/a
5	MTA3	chr10:38264161-38266087	GM12878	blood:	n/a	n/a
6	YY1	chr10:38264248-38264637	GM12878	blood:	n/a	chr10:38264427-38264437
7	POLR2A	chr10:38264006-38265982	NB4	blood:	n/a	n/a
8	MAX	chr10:38264191-38266090	NB4	blood:	n/a	n/a
9	NFYB	chr10:38264336-38264536	GM12878	blood:	n/a	chr10:38264391-38264406 chr10:38264390-38264402 chr10:38264391-38264405 chr10:38264393-38264403 chr10:38264391-38264406
10	PML	chr10:38264280-38266101	GM12878	blood:	n/a	n/a
11	POLR2A	chr10:38264352-38266040	GM12878	blood:	n/a	n/a
12	RUNX3	chr10:38264329-38264733	GM12878	blood:	n/a	chr10:38264562-38264571 chr10:38264562-38264571
13	YY1	chr10:38264293-38264601	GM12878	blood:	n/a	chr10:38264427-38264437
14	RCOR1	chr10:38264276-38265918	K562	blood:	n/a	n/a
15	POLR2A	chr10:38264359-38265938	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr10:38264335-38265920	HepG2	liver:	n/a	n/a
17	HCFC1	chr10:38264273-38266099	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr10:38264287-38266016	GM12891	blood:	n/a	n/a
19	POLR2A	chr10:38264332-38265997	GM12878	blood:	n/a	n/a
20	CEBPB	chr10:38264192-38264552	K562	blood:	n/a	chr10:38264394-38264402
21	RUNX3	chr10:38264274-38266012	GM12878	blood:	n/a	chr10:38264562-38264571 chr10:38264562-38264571
22	YY1	chr10:38264274-38264556	SK-N-SH_RA	brain:	n/a	chr10:38264427-38264437
23	RAD21	chr10:38264102-38266099	SK-N-SH	brain:	n/a	chr10:38265229-38265242 chr10:38265151-38265164 chr10:38265709-38265728
24	POLR2A	chr10:38264262-38266012	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr10:38264382-38265953	Raji	blood:	n/a	n/a
26	CTCF	chr10:38264377-38266234	A549	lung:	n/a	chr10:38265315-38265328 chr10:38265708-38265726 chr10:38265315-38265324 chr10:38265709-38265725 chr10:38265711-38265724
27	CEBPB	chr10:38264224-38264529	Hela-S3	cervix:	n/a	chr10:38264394-38264402
28	REST	chr10:38264202-38266267	H1-neurons	neurons:	n/a	chr10:38265720-38265729 chr10:38265354-38265367
29	YY1	chr10:38264298-38264646	GM12892	blood:	n/a	chr10:38264427-38264437
30	YY1	chr10:38264316-38264760	SK-N-SH	brain:	n/a	chr10:38264427-38264437

No.	Distal block	Cell Line	Cell type
1	chr10:38242058..38244138-chr10:38263364..38265414,2	K562	blood:
2	chr10:38262821..38267029-chr10:38297888..38300843,9	MCF-7	breast:
3	chr10:38260688..38263129-chr10:38263289..38264919,2	MCF-7	breast:
4	chr10:38259521..38261309-chr10:38263503..38265407,2	MCF-7	breast:
5	chr10:38144757..38148220-chr10:38264242..38266228,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226447	TF binding region
ENSG00000236514	Chromatin interaction
ENSG00000189180	Chromatin interaction
ENSG00000266684	Chromatin interaction
ENSG00000198105	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10827830	1.00[EUR][1000 genomes]
rs10827834	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10827837	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10827838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011356	1.00[EUR][1000 genomes]
rs11011364	1.00[EUR][1000 genomes]
rs11011368	0.89[EUR][1000 genomes]
rs11011375	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs11011376	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11011385	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011391	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11011393	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011403	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011412	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011417	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11011428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011429	1.00[EUR][1000 genomes]
rs11011430	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011437	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011438	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11812927	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11813723	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11813932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11814622	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11816307	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11816860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11817782	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11818933	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11819551	1.00[EUR][1000 genomes]
rs12240311	1.00[EUR][1000 genomes]
rs12241614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12242343	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12245586	1.00[EUR][1000 genomes]
rs12248857	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12250395	1.00[EUR][1000 genomes]
rs12251570	1.00[EUR][1000 genomes]
rs12252754	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12256181	1.00[EUR][1000 genomes]
rs12256794	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12256916	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12257902	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12258024	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs12258128	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12258252	1.00[EUR][1000 genomes]
rs12260189	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12260310	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12262814	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12262927	1.00[EUR][1000 genomes]
rs12266728	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12267847	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12269398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12770231	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12773340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12777107	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12778900	1.00[EUR][1000 genomes]
rs12779056	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2023432	1.00[EUR][1000 genomes]
rs34222428	1.00[EUR][1000 genomes]
rs34445730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34591573	1.00[EUR][1000 genomes]
rs34918037	1.00[EUR][1000 genomes]
rs34964888	1.00[EUR][1000 genomes]
rs35006520	1.00[EUR][1000 genomes]
rs35246660	1.00[EUR][1000 genomes]
rs35404142	1.00[EUR][1000 genomes]
rs57753536	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60538050	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71491203	1.00[EUR][1000 genomes]
rs71491210	1.00[EUR][1000 genomes]
rs71491212	1.00[EUR][1000 genomes]
rs71491214	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71491223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71491227	1.00[EUR][1000 genomes]
rs71491228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71491229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9651365	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS 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	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1051121	chr10:38155991-38426204	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv540565	chr10:38155991-38426204	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv1052703	chr10:38174640-38266472	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv534122	chr10:38240258-38356008	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38239600-38264400	Weak transcription	Fetal Heart	heart
2	chr10:38239600-38264600	Weak transcription	Stomach Mucosa	stomach
3	chr10:38241800-38264400	Weak transcription	NHEK	skin
4	chr10:38242600-38264400	Weak transcription	HUVEC	blood vessel
5	chr10:38246400-38264400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr10:38254200-38264400	Weak transcription	NH-A	brain
7	chr10:38254200-38264600	Weak transcription	Gastric	stomach
8	chr10:38254200-38264600	Weak transcription	Pancreas	Pancrea
9	chr10:38254400-38264400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr10:38254400-38264400	Weak transcription	Aorta	Aorta
11	chr10:38254800-38264600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr10:38255600-38264600	Weak transcription	Spleen	Spleen
13	chr10:38256600-38264600	Weak transcription	Lung	lung
14	chr10:38256800-38264600	Weak transcription	Placenta	Placenta
15	chr10:38256800-38264600	Weak transcription	Right Ventricle	heart
16	chr10:38257200-38264400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr10:38257400-38264400	Weak transcription	Fetal Intestine Small	intestine
18	chr10:38257400-38265000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr10:38258000-38264400	Weak transcription	HSMMtube	muscle
20	chr10:38258600-38264400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr10:38258600-38264400	Weak transcription	Osteobl	bone
22	chr10:38258600-38264600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr10:38258600-38264600	Weak transcription	Ovary	ovary
24	chr10:38259000-38264400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr10:38259400-38264400	Weak transcription	Fetal Intestine Large	intestine
26	chr10:38259400-38264400	Weak transcription	HSMM	muscle
27	chr10:38260000-38264400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr10:38260000-38264400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr10:38260000-38264400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr10:38260000-38264600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr10:38260200-38264400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr10:38260200-38264600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr10:38260400-38264400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:38260600-38264400	Weak transcription	Fetal Stomach	stomach
35	chr10:38260600-38264600	Weak transcription	Left Ventricle	heart
36	chr10:38260800-38264400	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr10:38260800-38264400	Weak transcription	Fetal Muscle Leg	muscle
38	chr10:38262400-38264600	Weak transcription	Esophagus	oesophagus
39	chr10:38263000-38264400	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr10:38263600-38264400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr10:38263600-38264400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr10:38263600-38264400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr10:38263600-38264400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr10:38263600-38264600	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr10:38263800-38264400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:38263800-38264400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr10:38263800-38264400	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr10:38263800-38264400	Enhancers	Brain Substantia Nigra	brain
49	chr10:38263800-38264400	Enhancers	Colon Smooth Muscle	Colon
50	chr10:38263800-38264400	Enhancers	Duodenum Mucosa	Duodenum

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