Variant report

Variant	rs13009725
Chromosome Location	chr2:85998858-85998859
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85997689..85999503-chr2:86015915..86018374,2	MCF-7	breast:
2	chr2:85997012..86000139-chr2:86001257..86004684,4	MCF-7	breast:
3	chr2:85998096..86001212-chr2:86021812..86025448,3	MCF-7	breast:
4	chr2:85995032..85998218-chr2:85998499..86001360,4	MCF-7	breast:
5	chr2:85981466..85983432-chr2:85998225..85999841,2	MCF-7	breast:
6	chr2:85962517..85964339-chr2:85996899..85999764,2	MCF-7	breast:
7	chr2:85984055..85985745-chr2:85996353..85999669,3	MCF-7	breast:
8	chr2:85998588..86002655-chr2:86008368..86012059,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168874	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11688843	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12989354	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1465821	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832010	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4832011	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4832012	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4832013	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4832194	0.83[EUR][1000 genomes]
rs4832197	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4832198	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59512984	0.88[ASN][1000 genomes]
rs67494720	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72928918	0.83[ASN][1000 genomes]
rs72928938	0.88[ASN][1000 genomes]
rs72928941	0.88[ASN][1000 genomes]
rs72928947	0.88[ASN][1000 genomes]
rs72928948	0.90[ASN][1000 genomes]
rs72928951	0.90[ASN][1000 genomes]
rs72928954	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874468	chr2:85926598-86001255	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers 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	6 gene(s)	inside rSNPs	diseases
2	nsv874469	chr2:85973618-86025251	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv874470	chr2:85973618-86028257	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv874471	chr2:85976645-86021919	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv1001792	chr2:85983107-86016722	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv535805	chr2:85983107-86016722	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
7	nsv535806	chr2:85990408-86007918	Enhancers Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85988600-86000000	Enhancers	Right Atrium	heart
2	chr2:85990800-85999800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr2:85991200-86000000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
4	chr2:85993400-86000000	Enhancers	Psoas Muscle	Psoas
5	chr2:85994000-86000400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:85994200-86000000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:85994400-85999000	Enhancers	Left Ventricle	heart
8	chr2:85994800-86002200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:85995000-85999000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:85995000-85999000	Enhancers	Colonic Mucosa	Colon
11	chr2:85995200-85999000	Enhancers	Fetal Muscle Leg	muscle
12	chr2:85995200-85999200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:85995200-85999800	Enhancers	NHDF-Ad	bronchial
14	chr2:85995200-86000600	Enhancers	Pancreas	Pancrea
15	chr2:85995400-85999000	Enhancers	Brain Germinal Matrix	brain
16	chr2:85995600-85999800	Enhancers	HUVEC	blood vessel
17	chr2:85995600-86000000	Enhancers	Ovary	ovary
18	chr2:85995600-86002200	Enhancers	Liver	Liver
19	chr2:85995800-86000200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr2:85995800-86001600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:85995800-86002000	Enhancers	Fetal Brain Male	brain
22	chr2:85996200-85999000	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr2:85996400-85999000	Enhancers	Fetal Brain Female	brain
24	chr2:85996600-85999600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:85996600-86000000	Enhancers	Fetal Heart	heart
26	chr2:85996800-85999000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:85996800-86000800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:85997000-85999200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:85997200-86000000	Enhancers	Right Ventricle	heart
30	chr2:85997400-85999800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:85997600-86000600	Enhancers	Lung	lung
32	chr2:85997800-85999000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
33	chr2:85997800-85999200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:85997800-86000000	Enhancers	Aorta	Aorta
35	chr2:85997800-86001000	Enhancers	Stomach Mucosa	stomach
36	chr2:85998000-85999000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:85998000-85999000	Enhancers	Fetal Kidney	kidney
38	chr2:85998000-85999000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
39	chr2:85998000-86000000	Enhancers	Fetal Intestine Small	intestine
40	chr2:85998000-86002000	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr2:85998200-85999200	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr2:85998200-85999200	Genic enhancers	NHLF	lung
43	chr2:85998200-85999400	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr2:85998200-86000200	Enhancers	Placenta	Placenta
45	chr2:85998200-86001000	Enhancers	Duodenum Mucosa	Duodenum
46	chr2:85998400-85999000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
47	chr2:85998400-85999000	Genic enhancers	Spleen	Spleen
48	chr2:85998400-85999200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:85998400-85999200	Bivalent Enhancer	Small Intestine	intestine
50	chr2:85998400-85999400	Flanking Active TSS	Colon Smooth Muscle	Colon

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