Variant report

Variant	rs4246709
Chromosome Location	chr4:79851880-79851881
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:79847059..79848626-chr4:79851803..79854574,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163291	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10028067	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10857058	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10857059	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1299129	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13123305	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13125525	0.90[ASN][1000 genomes]
rs1871706	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2903600	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534080	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843690	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657727	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664339	0.87[AMR][1000 genomes]
rs7664587	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677084	0.82[AMR][1000 genomes]
rs7690151	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307446	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv879504	chr4:79759796-79874275	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv829979	chr4:79819168-80019159	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1000907	chr4:79838948-80224764	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79779800-79858200	Weak transcription	Fetal Brain Male	brain
2	chr4:79794200-79859600	Weak transcription	Colonic Mucosa	Colon
3	chr4:79794800-79858000	Weak transcription	HepG2	liver
4	chr4:79799200-79858000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:79814600-79859600	Weak transcription	Fetal Kidney	kidney
6	chr4:79816200-79858400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr4:79827400-79858000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:79827400-79858000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr4:79829000-79859200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:79830200-79859200	Weak transcription	Hela-S3	cervix
11	chr4:79831200-79858000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:79831400-79856600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr4:79833000-79859800	Weak transcription	Esophagus	oesophagus
14	chr4:79833000-79859800	Weak transcription	Right Ventricle	heart
15	chr4:79833200-79853400	Weak transcription	NHLF	lung
16	chr4:79833200-79859000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:79833200-79859600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:79833400-79856800	Weak transcription	GM12878-XiMat	blood
19	chr4:79833600-79858000	Weak transcription	Brain Substantia Nigra	brain
20	chr4:79833600-79859000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:79833600-79859800	Weak transcription	Placenta	Placenta
22	chr4:79835600-79856000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:79836600-79859000	Weak transcription	HSMM	muscle
24	chr4:79840200-79856800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:79841600-79852200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:79841800-79857600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr4:79842000-79858200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr4:79843200-79853000	Strong transcription	Fetal Thymus	thymus
29	chr4:79843200-79854400	Strong transcription	Primary T cells from cord blood	blood
30	chr4:79843800-79855600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:79843800-79858800	Weak transcription	Brain Germinal Matrix	brain
32	chr4:79844200-79855800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:79844400-79852000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:79844400-79859000	Weak transcription	HUVEC	blood vessel
35	chr4:79844800-79855600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:79845000-79855000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:79845200-79859200	Weak transcription	Fetal Heart	heart
38	chr4:79845600-79856200	Weak transcription	Liver	Liver
39	chr4:79845800-79860000	Weak transcription	Small Intestine	intestine
40	chr4:79847000-79852000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr4:79847400-79858200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr4:79847600-79858800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr4:79848000-79858000	Weak transcription	Colon Smooth Muscle	Colon
44	chr4:79848000-79859000	Weak transcription	HMEC	breast
45	chr4:79848400-79858800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr4:79848400-79859000	Weak transcription	Brain Angular Gyrus	brain
47	chr4:79849200-79857600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr4:79849200-79858400	Weak transcription	Psoas Muscle	Psoas
49	chr4:79849200-79859000	Weak transcription	NH-A	brain
50	chr4:79849200-79859600	Weak transcription	Fetal Lung	lung

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