Variant report

Variant	rs6554281
Chromosome Location	chr4:56377898-56377899
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	POLR2A	chr4:56377709-56377929	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:56377264..56378786-chr4:56411943..56413816,2	MCF-7	breast:

Variant related genes	Relation type
CLOCK	TF binding region
ENSG00000134852	Chromatin interaction
ENSG00000272969	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs4631105	1.00[ASN][1000 genomes]
rs4864552	1.00[ASN][1000 genomes]
rs6554299	1.00[ASN][1000 genomes]
rs6822710	1.00[ASN][1000 genomes]
rs6828640	1.00[ASN][1000 genomes]
rs6838362	1.00[ASN][1000 genomes]
rs6856478	1.00[ASN][1000 genomes]
rs73236129	1.00[ASN][1000 genomes]
rs73236146	1.00[ASN][1000 genomes]
rs73236158	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56341400-56385600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:56342400-56378200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr4:56342800-56391400	Weak transcription	Psoas Muscle	Psoas
4	chr4:56344600-56378200	Weak transcription	Brain Germinal Matrix	brain
5	chr4:56355400-56378000	Weak transcription	Aorta	Aorta
6	chr4:56355400-56379200	Weak transcription	Ovary	ovary
7	chr4:56355400-56379200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:56355400-56380800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:56355400-56381800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr4:56355400-56386200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr4:56361200-56387400	Weak transcription	Left Ventricle	heart
12	chr4:56361400-56381000	Weak transcription	Fetal Brain Male	brain
13	chr4:56361600-56411800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:56361800-56384400	Weak transcription	Primary B cells from cord blood	blood
15	chr4:56366200-56386400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:56370000-56379200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:56370000-56379600	Weak transcription	NHDF-Ad	bronchial
18	chr4:56370000-56391200	Weak transcription	HSMM	muscle
19	chr4:56370200-56390800	Weak transcription	HMEC	breast
20	chr4:56372600-56405200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:56373600-56386000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:56374400-56379400	Weak transcription	A549	lung
23	chr4:56374400-56380200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:56374600-56379600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:56375400-56379400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:56375400-56385000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr4:56375600-56390000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:56375800-56378000	Weak transcription	Primary T cells from cord blood	blood
29	chr4:56375800-56384800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr4:56375800-56393800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:56376200-56378000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr4:56376200-56378000	Weak transcription	Placenta	Placenta
33	chr4:56376200-56384800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:56376200-56386000	Weak transcription	HepG2	liver
35	chr4:56376200-56391000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:56376400-56379200	Weak transcription	Osteobl	bone
37	chr4:56376400-56387400	Weak transcription	NHEK	skin
38	chr4:56376800-56378000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:56377200-56378000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:56377400-56378000	Enhancers	Stomach Mucosa	stomach
41	chr4:56377800-56378000	Enhancers	Gastric	stomach

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