Variant report

Variant	rs295944
Chromosome Location	chr5:58887194-58887195
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	STAT3	chr5:58887098-58887365	MCF10A-Er-Src	breast:	n/a	chr5:58887276-58887287
2	STAT3	chr5:58887048-58887378	MCF10A-Er-Src	breast:	n/a	chr5:58887276-58887287
3	FOS	chr5:58887088-58887369	MCF10A-Er-Src	breast:	n/a	n/a
4	EP300	chr5:58886953-58887394	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr5:58886998-58887255	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr5:58886832-58887426	MCF10A-Er-Src	breast:	n/a	chr5:58887276-58887287
7	PRDM1	chr5:58887088-58887445	Hela-S3	cervix:	n/a	chr5:58887275-58887288 chr5:58887273-58887288 chr5:58887274-58887288
8	EP300	chr5:58886865-58887384	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:58886770-58888662	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr5:58887098-58887367	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr5:58887087-58887403	Hela-S3	cervix:	n/a	n/a
12	FOS	chr5:58886940-58887502	MCF10A-Er-Src	breast:	n/a	n/a
13	RUNX3	chr5:58886988-58887437	GM12878	blood:	n/a	n/a
14	EP300	chr5:58887036-58887354	GM12878	blood:	n/a	n/a
15	BCL11A	chr5:58887084-58887368	GM12878	blood:	n/a	chr5:58887234-58887241 chr5:58887278-58887287
16	NFIC	chr5:58886988-58887488	GM12878	blood:	n/a	n/a
17	FOS	chr5:58886968-58887421	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr5:58887052-58887406	MCF10A-Er-Src	breast:	n/a	chr5:58887276-58887287
19	EP300	chr5:58887026-58887363	GM12878	blood:	n/a	n/a
20	RELA	chr5:58887028-58887396	GM12878	blood:	n/a	n/a
21	CUX1	chr5:58887063-58887522	GM12878	blood:	n/a	chr5:58887467-58887478
22	MYC	chr5:58886967-58887421	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10805516	0.86[CEU][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs159194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs159196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[ASN][1000 genomes]
rs159197	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs177077	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs177078	0.87[ASN][1000 genomes]
rs186078	0.91[ASN][1000 genomes]
rs190936	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs294477	0.91[ASN][1000 genomes]
rs294478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs294479	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs294481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs294482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs294483	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs294484	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs294485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs294486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs294492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs294494	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs294495	0.99[ASN][1000 genomes]
rs294496	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs294497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs294498	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs294499	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs294500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs294501	0.96[ASN][1000 genomes]
rs294502	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs295943	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295946	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs295948	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295950	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295951	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295952	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs295953	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295954	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295955	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295956	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295957	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295958	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295960	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295962	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295964	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295965	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295966	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295967	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295968	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295969	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295970	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295971	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295972	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs295974	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295975	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295978	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295979	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs295980	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298014	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs298016	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs298017	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs298025	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298027	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298028	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298029	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298030	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298032	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298033	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298034	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs298036	0.87[ASN][1000 genomes]
rs298038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs298039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs298040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs298041	0.87[ASN][1000 genomes]
rs298043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs298044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs298045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs298046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs298047	0.87[ASN][1000 genomes]
rs298048	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs298051	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs298052	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs298053	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs37569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs37570	0.92[ASN][1000 genomes]
rs37571	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[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	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58878800-58888200	Active TSS	Psoas Muscle	Psoas
2	chr5:58883800-58888800	Enhancers	Hela-S3	cervix
3	chr5:58883800-58894200	Weak transcription	Aorta	Aorta
4	chr5:58884000-58887800	Weak transcription	HSMMtube	muscle
5	chr5:58884200-58887200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr5:58884200-58888000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:58884200-58888000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:58884200-58892600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:58884200-58892600	Weak transcription	Osteobl	bone
10	chr5:58884200-58893800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr5:58884200-58894000	Weak transcription	Right Atrium	heart
12	chr5:58884200-58894200	Weak transcription	Liver	Liver
13	chr5:58884200-58902800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:58884400-58888000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:58884400-58889400	Weak transcription	Brain Angular Gyrus	brain
16	chr5:58884600-58888000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:58884600-58888000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:58884600-58888000	Weak transcription	Brain Anterior Caudate	brain
19	chr5:58884600-58892200	Weak transcription	Small Intestine	intestine
20	chr5:58884600-58892600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr5:58884600-58893800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr5:58884800-58887200	Weak transcription	Colon Smooth Muscle	Colon
23	chr5:58884800-58887800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:58884800-58888000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr5:58885000-58887800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:58885000-58887800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:58885000-58892200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:58885000-58894200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr5:58885200-58887800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:58885200-58892400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr5:58885200-58892800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:58885400-58887800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr5:58885400-58892200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:58885400-58892600	Weak transcription	HUVEC	blood vessel
35	chr5:58885600-58887200	Enhancers	Stomach Mucosa	stomach
36	chr5:58886000-58888400	Enhancers	Fetal Intestine Small	intestine
37	chr5:58886200-58888200	Enhancers	Primary B cells from peripheral blood	blood
38	chr5:58886200-58888200	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr5:58886600-58887400	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr5:58886600-58888200	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr5:58886800-58888000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:58886800-58892800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:58887000-58887200	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr5:58887000-58887200	Enhancers	Fetal Lung	lung
45	chr5:58887000-58887200	Flanking Active TSS	A549	lung
46	chr5:58887000-58887400	Active TSS	Brain Substantia Nigra	brain
47	chr5:58887000-58887400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr5:58887000-58887400	Flanking Active TSS	NHEK	skin
49	chr5:58887000-58887600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:58887000-58887800	Weak transcription	Rectal Mucosa Donor 29	rectum

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