Variant report

Variant	rs2609858
Chromosome Location	chr3:146262021-146262022
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:146234591..146236203-chr3:146259470..146262375,2	MCF-7	breast:
2	chr19:32896461..32897385-chr3:146261852..146262365,2	Hela-S3	cervix:
3	chr3:146254115..146256698-chr3:146261297..146263941,3	MCF-7	breast:
4	chr17:7387396..7387925-chr3:146261229..146262098,2	Hela-S3	cervix:
5	chr3:146237235..146239692-chr3:146260498..146262293,2	K562	blood:
6	chr3:146261960..146262783-chr8:98787677..98788425,2	Hela-S3	cervix:
7	chr3:146234146..146236591-chr3:146261590..146264248,2	K562	blood:
8	chr3:146251866..146257697-chr3:146260468..146262994,8	MCF-7	breast:
9	chr2:170550671..170551359-chr3:146261829..146262448,2	Hela-S3	cervix:
10	chr3:146234740..146236294-chr3:146259809..146262278,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000144362	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000178904	Chromatin interaction
ENSG00000213160	Chromatin interaction
ENSG00000154479	Chromatin interaction
ENSG00000267213	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000104341	Chromatin interaction
ENSG00000188313	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1057481	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1061307	0.89[AFR][1000 genomes]
rs1079369	0.99[ASN][1000 genomes]
rs13064509	0.96[ASN][1000 genomes]
rs13069082	0.94[ASN][1000 genomes]
rs1373246	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1443827	0.94[ASN][1000 genomes]
rs1882971	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1882972	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1882973	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1882974	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1997601	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1997604	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2120381	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2165948	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2587007	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2587008	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2587009	0.93[ASN][1000 genomes]
rs2587010	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2587011	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2587012	0.92[ASN][1000 genomes]
rs2587013	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2587014	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2587015	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2587016	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2587017	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2587018	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2587023	0.91[ASN][1000 genomes]
rs2587024	0.91[ASN][1000 genomes]
rs2609860	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2609861	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2609862	0.92[ASN][1000 genomes]
rs2609864	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2609865	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2609866	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2609867	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2688688	0.91[ASN][1000 genomes]
rs2738905	0.91[ASN][1000 genomes]
rs2738906	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2738907	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2738910	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2738911	0.93[ASN][1000 genomes]
rs2738912	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2738915	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2738916	0.92[ASN][1000 genomes]
rs2738918	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2738920	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2738923	0.92[ASN][1000 genomes]
rs35214899	0.96[ASN][1000 genomes]
rs35309521	0.84[ASN][1000 genomes]
rs3773510	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs67703040	0.92[ASN][1000 genomes]
rs7615988	0.96[ASN][1000 genomes]
rs9289722	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs977758	0.94[ASN][1000 genomes]
rs9861142	0.96[ASN][1000 genomes]
rs9865918	0.96[ASN][1000 genomes]
rs9876886	0.99[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	esv3448053	chr3:146186791-146262066	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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	13 gene(s)	inside rSNPs	diseases
2	esv2496437	chr3:146186902-146262961	Enhancers Active TSS Genic enhancers Weak transcription 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	18 gene(s)	inside rSNPs	diseases
3	nsv1014493	chr3:146255594-146288414	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146258000-146263200	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr3:146258400-146263200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:146258800-146262200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:146258800-146263000	Active TSS	Brain Anterior Caudate	brain
5	chr3:146258800-146263000	Active TSS	Ovary	ovary
6	chr3:146259200-146262800	Active TSS	Brain Hippocampus Middle	brain
7	chr3:146259200-146263200	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr3:146259200-146263200	Active TSS	Right Ventricle	heart
9	chr3:146259400-146263000	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr3:146259600-146262800	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr3:146259600-146263000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:146259600-146263000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:146259800-146262800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:146259800-146262800	Active TSS	Psoas Muscle	Psoas
15	chr3:146259800-146263000	Active TSS	Fetal Muscle Leg	muscle
16	chr3:146259800-146263200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:146259800-146263200	Active TSS	Colonic Mucosa	Colon
18	chr3:146260000-146263000	Active TSS	Liver	Liver
19	chr3:146260000-146263000	Active TSS	Fetal Stomach	stomach
20	chr3:146260000-146263200	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr3:146260000-146263200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:146260200-146262800	Active TSS	Brain Angular Gyrus	brain
23	chr3:146260200-146262800	Active TSS	Pancreas	Pancrea
24	chr3:146260200-146262800	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr3:146260200-146263000	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr3:146260200-146263000	Active TSS	GM12878-XiMat	blood
27	chr3:146260200-146263000	Active TSS	Hela-S3	cervix
28	chr3:146260200-146263200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:146260400-146263000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:146260400-146263000	Active TSS	Fetal Intestine Large	intestine
31	chr3:146260400-146263000	Active TSS	Fetal Intestine Small	intestine
32	chr3:146260400-146263000	Active TSS	Rectal Smooth Muscle	rectum
33	chr3:146260600-146262400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:146260600-146263000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr3:146260800-146262200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:146260800-146262800	Active TSS	Brain Substantia Nigra	brain
37	chr3:146260800-146262800	Active TSS	Gastric	stomach
38	chr3:146260800-146262800	Active TSS	Left Ventricle	heart
39	chr3:146260800-146262800	Active TSS	Lung	lung
40	chr3:146260800-146262800	Active TSS	Stomach Mucosa	stomach
41	chr3:146260800-146263000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr3:146260800-146263000	Active TSS	Placenta	Placenta
43	chr3:146260800-146263000	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr3:146260800-146263000	Active TSS	Thymus	Thymus
45	chr3:146260800-146263000	Active TSS	HSMMtube	muscle
46	chr3:146260800-146263200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:146260800-146263400	Active TSS	HSMM	muscle
48	chr3:146261000-146262200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr3:146261000-146262800	Active TSS	Aorta	Aorta
50	chr3:146261000-146262800	Active TSS	Esophagus	oesophagus

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