Variant report

Variant	rs12517786
Chromosome Location	chr5:95295687-95295688
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	CTCF	chr5:95295621-95296138	K562	blood:	n/a	n/a
2	MXI1	chr5:95295550-95298162	HepG2	liver:	n/a	n/a
3	RAD21	chr5:95295642-95296224	Hela-S3	cervix:	n/a	n/a
4	RAD21	chr5:95295552-95298217	IMR90	lung:	n/a	chr5:95296846-95296859 chr5:95297062-95297075 chr5:95296847-95296861 chr5:95297059-95297078
5	POLR2A	chr5:95294827-95298308	GM12892	blood:	n/a	n/a
6	RELA	chr5:95294993-95298352	GM12891	blood:	n/a	chr5:95297005-95297014 chr5:95297005-95297014
7	GATA3	chr5:95294863-95295873	SK-N-SH	brain:	n/a	chr5:95295170-95295179
8	POLR2A	chr5:95294649-95297075	HepG2	liver:	n/a	n/a
9	PML	chr5:95295247-95298289	GM12878	blood:	n/a	chr5:95296249-95296257
10	RAD21	chr5:95295600-95296005	HepG2	liver:	n/a	n/a
11	POLR2A	chr5:95294744-95298231	GM12891	blood:	n/a	n/a
12	ELK1	chr5:95295491-95295971	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr5:95294626-95298807	GM12892	blood:	n/a	n/a
14	POLR2A	chr5:95294626-95298519	GM12892	blood:	n/a	n/a
15	POLR2A	chr5:95295651-95298283	GM18951	blood:	n/a	n/a
16	POLR2A	chr5:95293827-95297878	ProgFib	skin:	n/a	n/a
17	POLR2A	chr5:95294579-95298340	GM12878	blood:	n/a	n/a
18	POLR2A	chr5:95293418-95298067	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr5:95295338-95296055	SK-N-SH	brain:	n/a	n/a
20	SMC3	chr5:95295595-95297958	Hela-S3	cervix:	n/a	chr5:95297064-95297074 chr5:95297060-95297074
21	MAZ	chr5:95295254-95295879	K562	blood:	n/a	n/a
22	POLR2A	chr5:95293281-95298477	GM12891	blood:	n/a	n/a
23	POLR2A	chr5:95295376-95298425	GM15510	blood:	n/a	n/a
24	POLR2A	chr5:95295384-95295754	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr5:95293681-95298523	MCF10A-Er-Src	breast:	n/a	n/a
26	CTCF	chr5:95295660-95295810	SK-N-SH_RA	brain:	n/a	n/a
27	POLR2A	chr5:95294788-95297231	A549	lung:	n/a	n/a
28	CTCF	chr5:95295660-95295810	NHLF	lung:	n/a	n/a
29	SMARCB1	chr5:95295610-95298225	Hela-S3	cervix:	n/a	chr5:95296156-95296165
30	MXI1	chr5:95295438-95295777	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr5:95295377-95296570	U87	brain:	n/a	n/a
32	CTCF	chr5:95295680-95295830	HepG2	liver:	n/a	n/a
33	POLR2A	chr5:95294916-95298224	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr5:95295362-95297695	GM12891	blood:	n/a	n/a
35	CTCF	chr5:95295680-95295830	HPAF	blood vessel:	n/a	n/a
36	CTCF	chr5:95295316-95297628	SK-N-SH	brain:	n/a	chr5:95297058-95297076 chr5:95297061-95297070 chr5:95297061-95297074
37	POLR2A	chr5:95294709-95297866	Hela-S3	cervix:	n/a	n/a
38	CTCF	chr5:95295680-95295830	GM12801	blood:	n/a	n/a
39	POLR2A	chr5:95294702-95296246	HepG2	liver:	n/a	n/a
40	WRNIP1	chr5:95293706-95297115	GM12878	blood:	n/a	n/a
41	E2F6	chr5:95295639-95297483	K562	blood:	n/a	chr5:95297196-95297206 chr5:95297056-95297065
42	MAX	chr5:95294946-95297886	Hela-S3	cervix:	n/a	n/a
43	MTA3	chr5:95295399-95296284	GM12878	blood:	n/a	n/a
44	POLR2A	chr5:95293433-95298625	PBDE	blood:	n/a	n/a
45	POLR2A	chr5:95294723-95298270	GM19193	blood:	n/a	n/a
46	POLR2A	chr5:95294699-95298270	GM18505	blood:	n/a	n/a
47	CHD1	chr5:95290276-95298838	IMR90	lung:	n/a	chr5:95296574-95296584
48	MAX	chr5:95295203-95296107	GM12878	blood:	n/a	n/a
49	CTCF	chr5:95295560-95295710	GM12872	blood:	n/a	n/a
50	CTCF	chr5:95295642-95295870	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:95233131..95236035-chr5:95293945..95295871,2	MCF-7	breast:
2	chr5:95294090..95296695-chr5:95356956..95358736,2	K562	blood:
3	chr5:95268201..95271259-chr5:95293634..95296677,4	K562	blood:
4	chr5:95294561..95296390-chr5:95300649..95302787,2	MCF-7	breast:
5	chr5:95294921..95295995-chr5:95671820..95672599,4	MCF-7	breast:
6	chr5:95265302..95267698-chr5:95294461..95296344,2	K562	blood:
7	chr5:95294835..95302887-chr5:95306601..95313873,11	K562	blood:
8	chr5:95284805..95286720-chr5:95295035..95296550,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251314	TF binding region
ENSG00000118985	Chromatin interaction
ENSG00000213716	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10428657	1.00[EUR][1000 genomes]
rs10428702	1.00[EUR][1000 genomes]
rs10515233	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515234	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948037	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12514472	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12514954	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12522489	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523306	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17085220	1.00[EUR][1000 genomes]
rs17085223	1.00[EUR][1000 genomes]
rs17085224	1.00[EUR][1000 genomes]
rs17085227	1.00[EUR][1000 genomes]
rs17085243	1.00[EUR][1000 genomes]
rs17085339	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17085366	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17085373	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17085393	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17085426	1.00[EUR][1000 genomes]
rs28521883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756701	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777174	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3777176	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777177	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777180	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41276261	1.00[EUR][1000 genomes]
rs55763081	1.00[EUR][1000 genomes]
rs56776515	1.00[EUR][1000 genomes]
rs58389685	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60908902	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61268106	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6143071	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6556897	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861075	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6870388	1.00[EUR][1000 genomes]
rs6872006	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874371	1.00[EUR][1000 genomes]
rs6891082	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891633	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893788	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73771827	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7700606	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7724475	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736480	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9687631	1.00[EUR][1000 genomes]
rs977128	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977129	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95290600-95296800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
2	chr5:95291200-95296000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:95291400-95296200	Transcr. at gene 5' and 3'	HMEC	breast
4	chr5:95292600-95296000	Transcr. at gene 5' and 3'	HSMM	muscle
5	chr5:95293000-95296600	Transcr. at gene 5' and 3'	NHEK	skin
6	chr5:95293800-95295800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:95293800-95295800	Enhancers	Primary B cells from peripheral blood	blood
8	chr5:95293800-95296200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:95293800-95296600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:95293800-95296800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:95293800-95296800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
12	chr5:95293800-95297800	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr5:95294000-95295800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:95294000-95295800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:95294000-95295800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:95294000-95296000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:95294000-95297400	Bivalent/Poised TSS	HepG2	liver
18	chr5:95294000-95298000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:95294000-95298000	Active TSS	Rectal Smooth Muscle	rectum
20	chr5:95294200-95296200	Transcr. at gene 5' and 3'	NHLF	lung
21	chr5:95294400-95295800	Flanking Active TSS	Osteobl	bone
22	chr5:95294400-95296000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:95294400-95296200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:95294400-95297800	Active TSS	HSMMtube	muscle
25	chr5:95294400-95298600	Active TSS	Aorta	Aorta
26	chr5:95294600-95295800	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr5:95294600-95296400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:95294600-95298000	Active TSS	Brain Angular Gyrus	brain
29	chr5:95294600-95298200	Active TSS	Fetal Intestine Large	intestine
30	chr5:95294600-95298200	Active TSS	GM12878-XiMat	blood
31	chr5:95294600-95298400	Active TSS	Brain Substantia Nigra	brain
32	chr5:95294800-95295800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr5:95294800-95295800	Genic enhancers	Spleen	Spleen
34	chr5:95294800-95295800	Flanking Active TSS	A549	lung
35	chr5:95294800-95296000	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr5:95294800-95296000	Enhancers	Primary T cells fromperipheralblood	blood
37	chr5:95294800-95296000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:95294800-95296000	Flanking Active TSS	Fetal Stomach	stomach
39	chr5:95294800-95296200	Flanking Active TSS	Placenta	Placenta
40	chr5:95294800-95296400	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr5:95294800-95296400	Flanking Active TSS	Fetal Brain Male	brain
42	chr5:95294800-95296400	Flanking Active TSS	K562	blood
43	chr5:95294800-95296600	Flanking Active TSS	Fetal Thymus	thymus
44	chr5:95294800-95297000	Transcr. at gene 5' and 3'	Pancreatic Islets	Pancreatic Islet
45	chr5:95294800-95297000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr5:95295000-95295800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr5:95295000-95295800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr5:95295000-95295800	Bivalent Enhancer	Fetal Muscle Leg	muscle
49	chr5:95295000-95295800	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr5:95295000-95296000	Flanking Active TSS	Stomach Mucosa	stomach

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