Variant report

Variant	rs55852678
Chromosome Location	chr3:50604684-50604685
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	chr3:50604580-50604730	HPAF	blood vessel:	n/a	n/a
2	NFYB	chr3:50604666-50605730	GM12878	blood:	n/a	chr3:50605211-50605226 chr3:50605211-50605226 chr3:50605213-50605228 chr3:50605212-50605226
3	CTCF	chr3:50604560-50604710	HCPEpiC	choroid plexus:	n/a	n/a
4	GTF2F1	chr3:50604641-50604766	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAZ	chr3:50604593-50604751	Hela-S3	cervix:	n/a	n/a
6	NRF1	chr3:50604670-50605418	GM12878	blood:	n/a	chr3:50605199-50605208
7	TCF7L2	chr3:50604625-50604722	Hela-S3	cervix:	n/a	n/a
8	NFYA	chr3:50604673-50605560	K562	blood:	n/a	chr3:50605211-50605226 chr3:50605211-50605226 chr3:50605207-50605225 chr3:50605212-50605226
9	NFYB	chr3:50604661-50605570	K562	blood:	n/a	chr3:50605211-50605226 chr3:50605211-50605226 chr3:50605213-50605228 chr3:50605212-50605226
10	TFAP2C	chr3:50604348-50605601	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr3:50604620-50604770	BJ	skin:	n/a	n/a
12	CTCF	chr3:50604540-50604690	SK-N-SH_RA	brain:	n/a	n/a
13	PBX3	chr3:50604654-50605680	SK-N-SH	brain:	n/a	chr3:50605214-50605223 chr3:50605248-50605268
14	CTCF	chr3:50604640-50604790	A549	lung:	n/a	n/a
15	CTCF	chr3:50604620-50604770	Hela-S3	cervix:	n/a	n/a
16	SMARCB1	chr3:50604580-50605538	Hela-S3	cervix:	n/a	n/a
17	MAX	chr3:50604649-50605352	Hela-S3	cervix:	n/a	chr3:50605204-50605214
18	POLR2A	chr3:50604671-50605603	U87	brain:	n/a	n/a
19	POLR2A	chr3:50604671-50605597	U87	brain:	n/a	n/a
20	TFAP2A	chr3:50604319-50605531	Hela-S3	cervix:	n/a	chr3:50605149-50605163 chr3:50605147-50605162 chr3:50605200-50605212
21	MAZ	chr3:50604459-50605969	IMR90	lung:	n/a	chr3:50605204-50605214
22	CTBP2	chr3:50604615-50605431	H1-hESC	embryonic stem cell:	n/a	n/a
23	RCOR1	chr3:50604582-50604862	Hela-S3	cervix:	n/a	n/a
24	ELF1	chr3:50604486-50605509	GM12878	blood:	n/a	chr3:50604834-50604843
25	CTCF	chr3:50604580-50604730	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:50601751..50604727-chr3:50606251..50610444,5	MCF-7	breast:
2	chr3:50603678..50606532-chr3:50606738..50608762,2	K562	blood:
3	chr3:50567522..50569700-chr3:50602226..50604974,2	K562	blood:
4	chr3:50402920..50405878-chr3:50604369..50606579,2	K562	blood:
5	chr3:50597009..50601269-chr3:50602729..50605113,3	K562	blood:
6	chr3:50599337..50613537-chr3:50634306..50660129,118	MCF-7	breast:
7	chr3:50601756..50613871-chr3:50647072..50654542,28	K562	blood:
8	chr3:50590507..50593503-chr3:50601894..50604757,2	K562	blood:
9	chr3:50603678..50606671-chr3:50607262..50609999,2	K562	blood:

Variant related genes	Relation type
HEMK1	TF binding region
ENSG00000088543	Chromatin interaction
ENSG00000114738	Chromatin interaction
ENSG00000007402	Chromatin interaction
ENSG00000271858	Chromatin interaction
ENSG00000114737	Chromatin interaction
ENSG00000114735	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1038415	1.00[EUR][1000 genomes]
rs107457	1.00[EUR][1000 genomes]
rs1552255	1.00[EUR][1000 genomes]
rs1552256	1.00[EUR][1000 genomes]
rs17051012	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051016	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051017	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051404	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1843073	1.00[EUR][1000 genomes]
rs2232251	1.00[EUR][1000 genomes]
rs2355337	1.00[EUR][1000 genomes]
rs2459450	1.00[EUR][1000 genomes]
rs2609015	1.00[EUR][1000 genomes]
rs2609027	1.00[EUR][1000 genomes]
rs2675781	1.00[EUR][1000 genomes]
rs2675785	1.00[EUR][1000 genomes]
rs2675823	1.00[EUR][1000 genomes]
rs2675824	1.00[EUR][1000 genomes]
rs2675826	1.00[EUR][1000 genomes]
rs2675833	1.00[EUR][1000 genomes]
rs407164	1.00[EUR][1000 genomes]
rs421689	1.00[EUR][1000 genomes]
rs4234694	1.00[EUR][1000 genomes]
rs4234695	1.00[EUR][1000 genomes]
rs4267639	1.00[EUR][1000 genomes]
rs4340700	1.00[EUR][1000 genomes]
rs4560294	1.00[AMR][1000 genomes]
rs4688704	1.00[EUR][1000 genomes]
rs55723661	1.00[AMR][1000 genomes]
rs56112107	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56198179	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56341000	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56413944	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57077411	1.00[AMR][1000 genomes]
rs57155820	1.00[AMR][1000 genomes]
rs57756789	1.00[EUR][1000 genomes]
rs57867785	1.00[AMR][1000 genomes]
rs57987466	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58231937	1.00[AMR][1000 genomes]
rs58854038	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58911362	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59065723	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59337835	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59340349	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59486246	1.00[AMR][1000 genomes]
rs60132317	1.00[EUR][1000 genomes]
rs60455882	1.00[EUR][1000 genomes]
rs609678	1.00[EUR][1000 genomes]
rs61032466	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61455710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs621975	1.00[EUR][1000 genomes]
rs628865	1.00[EUR][1000 genomes]
rs6446223	1.00[EUR][1000 genomes]
rs650473	1.00[EUR][1000 genomes]
rs665943	1.00[EUR][1000 genomes]
rs6768539	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6789552	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833231	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833232	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833239	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833242	1.00[AMR][1000 genomes]
rs73833247	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833248	1.00[AMR][1000 genomes]
rs73833404	1.00[AMR][1000 genomes]
rs73833406	1.00[AMR][1000 genomes]
rs73833886	1.00[AMR][1000 genomes]
rs73833935	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833940	1.00[AMR][1000 genomes]
rs73835518	1.00[EUR][1000 genomes]
rs73835533	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73835535	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73835537	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73835538	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936714	1.00[EUR][1000 genomes]
rs9840476	1.00[EUR][1000 genomes]
rs9857033	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50601600-50604800	Weak transcription	HMEC	breast
2	chr3:50603800-50604800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
3	chr3:50604000-50604800	Flanking Active TSS	Brain Angular Gyrus	brain
4	chr3:50604000-50605000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:50604000-50606000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr3:50604000-50606400	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr3:50604200-50604800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
8	chr3:50604200-50604800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:50604200-50604800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr3:50604200-50604800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:50604200-50604800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:50604200-50604800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:50604200-50604800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr3:50604200-50604800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:50604200-50604800	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr3:50604200-50604800	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr3:50604200-50604800	Flanking Active TSS	Brain Substantia Nigra	brain
18	chr3:50604200-50604800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
19	chr3:50604200-50604800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr3:50604200-50604800	Flanking Active TSS	Fetal Brain Male	brain
21	chr3:50604200-50604800	Flanking Active TSS	Fetal Brain Female	brain
22	chr3:50604200-50604800	Enhancers	Gastric	stomach
23	chr3:50604200-50604800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr3:50604200-50604800	Flanking Active TSS	Rectal Smooth Muscle	rectum
25	chr3:50604200-50604800	Flanking Active TSS	Right Ventricle	heart
26	chr3:50604200-50604800	Flanking Active TSS	Hela-S3	cervix
27	chr3:50604200-50604800	Flanking Active TSS	NHDF-Ad	bronchial
28	chr3:50604200-50604800	Flanking Active TSS	Osteobl	bone
29	chr3:50604200-50605000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr3:50604200-50605000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:50604200-50605000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:50604200-50605000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr3:50604200-50605800	Flanking Active TSS	Colonic Mucosa	Colon
34	chr3:50604200-50606200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr3:50604200-50606400	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr3:50604200-50606600	Flanking Active TSS	Dnd41	blood
37	chr3:50604200-50608400	Active TSS	H9 Cell Line	embryonic stem cell
38	chr3:50604400-50604800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:50604400-50604800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:50604400-50604800	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr3:50604400-50604800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
42	chr3:50604400-50604800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr3:50604400-50604800	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr3:50604400-50604800	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr3:50604400-50604800	Enhancers	Esophagus	oesophagus
46	chr3:50604400-50604800	Flanking Active TSS	Fetal Lung	lung
47	chr3:50604400-50604800	Flanking Active TSS	Ovary	ovary
48	chr3:50604400-50604800	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr3:50604400-50604800	Enhancers	Stomach Mucosa	stomach
50	chr3:50604400-50604800	Flanking Active TSS	Spleen	Spleen

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