Variant report

Variant	rs6825177
Chromosome Location	chr4:82394604-82394605
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	MAX	chr4:82394566-82394703	NB4	blood:	n/a	n/a
2	POLR2A	chr4:82391429-82394854	Raji	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:82392247..82394728-chr4:83351803..83353310,2	MCF-7	breast:

Variant related genes	Relation type
RASGEF1B	TF binding region
ENSG00000145293	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10010140	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10010394	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012642	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10015146	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10023826	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12500201	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12502814	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13102560	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13111699	1.00[ASN][1000 genomes]
rs13128387	0.90[ASN][1000 genomes]
rs13131664	0.95[ASN][1000 genomes]
rs16998600	0.97[ASN][1000 genomes]
rs17005142	1.00[ASN][1000 genomes]
rs17005144	1.00[ASN][1000 genomes]
rs17005145	1.00[ASN][1000 genomes]
rs28479652	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28767523	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28827174	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34128580	1.00[ASN][1000 genomes]
rs34749111	0.90[ASN][1000 genomes]
rs35010226	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35149381	0.95[ASN][1000 genomes]
rs35991185	1.00[ASN][1000 genomes]
rs36026752	1.00[ASN][1000 genomes]
rs41523946	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4693274	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693275	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4693276	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4693277	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62303604	1.00[ASN][1000 genomes]
rs6535252	1.00[ASN][1000 genomes]
rs6819741	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819989	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834665	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7660392	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7667427	0.90[AFR][1000 genomes]
rs7678464	0.90[ASN][1000 genomes]
rs7683852	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7684580	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688827	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7690069	0.95[ASN][1000 genomes]
rs7691170	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9307784	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[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	nsv999729	chr4:81802554-82627820	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537156	chr4:81802554-82627820	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv829986	chr4:82345163-82509860	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:82393600-82394800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr4:82393800-82394800	Enhancers	Fetal Thymus	thymus
3	chr4:82393800-82395200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr4:82393800-82395400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:82393800-82395400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:82393800-82395400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:82393800-82395600	Enhancers	Gastric	stomach
8	chr4:82393800-82395800	Enhancers	Colon Smooth Muscle	Colon
9	chr4:82393800-82396000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr4:82393800-82396000	Enhancers	Stomach Mucosa	stomach
11	chr4:82394000-82394800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:82394000-82394800	Enhancers	Duodenum Mucosa	Duodenum
13	chr4:82394000-82395000	Enhancers	Primary T cells fromperipheralblood	blood
14	chr4:82394000-82395000	Enhancers	Rectal Smooth Muscle	rectum
15	chr4:82394000-82395200	Enhancers	Brain Substantia Nigra	brain
16	chr4:82394000-82395400	Enhancers	Placenta	Placenta
17	chr4:82394000-82396600	Weak transcription	Fetal Kidney	kidney
18	chr4:82394200-82394800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr4:82394200-82395000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr4:82394200-82395000	Enhancers	Brain Hippocampus Middle	brain
21	chr4:82394200-82395200	Enhancers	Primary B cells from cord blood	blood
22	chr4:82394200-82395400	Enhancers	Primary B cells from peripheral blood	blood
23	chr4:82394400-82394800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr4:82394400-82394800	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr4:82394400-82395400	Enhancers	Stomach Smooth Muscle	stomach
26	chr4:82394400-82395600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:82394400-82395800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr4:82394600-82394800	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr4:82394600-82394800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr4:82394600-82394800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr4:82394600-82395000	Enhancers	H1 Cell Line	embryonic stem cell
32	chr4:82394600-82395000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:82394600-82395200	Enhancers	Liver	Liver
34	chr4:82394600-82395400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:82394600-82395400	Weak transcription	Colonic Mucosa	Colon
36	chr4:82394600-82395600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:82394600-82395600	Weak transcription	Esophagus	oesophagus
38	chr4:82394600-82395600	Enhancers	Lung	lung

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