Variant report

Variant	rs7589908
Chromosome Location	chr2:46846413-46846414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:46846363-46846542	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:46845368..46847323-chr2:47016580..47018230,2	K562	blood:
2	chr2:46845600..46848148-chr2:46860947..46862599,2	K562	blood:
3	chr2:46843822..46846111-chr2:46846206..46848342,2	K562	blood:
4	chr2:46768098..46772914-chr2:46841294..46848059,11	K562	blood:
5	chr2:46844525..46846523-chr2:46850500..46852298,2	MCF-7	breast:
6	chr2:46845764..46848148-chr2:46860387..46862849,3	K562	blood:
7	chr2:46768338..46773881-chr2:46842376..46848059,6	K562	blood:
8	chr2:46846051..46848798-chr2:46875763..46878074,2	K562	blood:
9	chr2:46788951..46790463-chr2:46844313..46846805,2	K562	blood:

No data

Variant related genes	Relation type
PIGF	TF binding region
ENSG00000119878	Chromatin interaction
ENSG00000119729	Chromatin interaction
ENSG00000151665	Chromatin interaction
ENSG00000250565	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1057899	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060656	1.00[ASN][1000 genomes]
rs11306	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1137748	1.00[ASN][1000 genomes]
rs11901678	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903907	0.87[ASN][1000 genomes]
rs13404342	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13406609	1.00[ASN][1000 genomes]
rs13410076	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1376406	1.00[ASN][1000 genomes]
rs1456018	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035272	0.87[ASN][1000 genomes]
rs17035361	1.00[ASN][1000 genomes]
rs1809087	0.87[ASN][1000 genomes]
rs2276554	0.97[ASN][1000 genomes]
rs3213985	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768723	1.00[ASN][1000 genomes]
rs3768724	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4300884	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4377377	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57134465	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57955462	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58101879	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58342271	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59183773	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59823825	0.87[ASN][1000 genomes]
rs60211996	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60738814	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61252474	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6544904	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544908	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6713104	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719813	1.00[ASN][1000 genomes]
rs6727471	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733143	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756134	1.00[ASN][1000 genomes]
rs68104662	0.93[ASN][1000 genomes]
rs72875696	0.87[ASN][1000 genomes]
rs7563577	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591561	0.87[ASN][1000 genomes]
rs7592446	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs962467	0.87[ASN][1000 genomes]
rs9808496	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
9	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46844600-46847200	Weak transcription	Spleen	Spleen
2	chr2:46844800-46847200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:46844800-46847200	Weak transcription	Lung	lung
4	chr2:46844800-46865600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:46844800-46868400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:46844800-46868400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:46844800-46868800	Weak transcription	Esophagus	oesophagus
8	chr2:46844800-46872200	Weak transcription	Pancreas	Pancrea
9	chr2:46845000-46847000	Weak transcription	Left Ventricle	heart
10	chr2:46845200-46846800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:46845200-46846800	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr2:46845200-46846800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:46845200-46846800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:46845200-46846800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:46845200-46847000	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:46845200-46847200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:46845200-46847200	Weak transcription	Gastric	stomach
18	chr2:46845200-46847200	Weak transcription	Ovary	ovary
19	chr2:46845200-46847400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:46845200-46847800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:46845200-46850000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:46845200-46854000	Weak transcription	Colonic Mucosa	Colon
23	chr2:46845400-46846800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:46845400-46846800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:46845400-46846800	Weak transcription	Fetal Intestine Large	intestine
26	chr2:46845400-46846800	Weak transcription	Fetal Thymus	thymus
27	chr2:46845400-46846800	Weak transcription	Thymus	Thymus
28	chr2:46845400-46846800	Weak transcription	HSMMtube	muscle
29	chr2:46845400-46846800	Weak transcription	NH-A	brain
30	chr2:46845400-46847000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
31	chr2:46845400-46847000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:46845400-46847000	Weak transcription	Fetal Kidney	kidney
33	chr2:46845400-46854000	Weak transcription	Small Intestine	intestine
34	chr2:46845400-46858400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr2:46845400-46864800	Weak transcription	Psoas Muscle	Psoas
36	chr2:46845400-46867000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:46845400-46871000	Weak transcription	Stomach Mucosa	stomach
38	chr2:46845400-46873000	Weak transcription	Right Ventricle	heart
39	chr2:46845600-46846800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:46845600-46846800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:46845600-46846800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:46845600-46846800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:46845600-46846800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr2:46845600-46846800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:46845600-46846800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:46845600-46846800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr2:46845600-46846800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr2:46845600-46847000	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr2:46845600-46847000	Weak transcription	GM12878-XiMat	blood
50	chr2:46845600-46847200	Weak transcription	Fetal Stomach	stomach

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