Variant report

Variant	rs3809330
Chromosome Location	chr13:48669064-48669065
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:48668651..48670754-chr13:48805441..48808765,3	MCF-7	breast:
2	chr13:48667865..48670263-chr13:48806295..48809101,2	MCF-7	breast:
3	chr13:48610643..48613395-chr13:48668732..48670612,2	MCF-7	breast:
4	chr13:48611740..48612388-chr13:48668929..48669462,3	MCF-7	breast:
5	chr13:48667088..48669248-chr13:48807095..48809011,2	K562	blood:
6	chr13:48669034..48669606-chr2:28974699..28975279,2	Hela-S3	cervix:
7	chr13:48651976..48654376-chr13:48667767..48670618,2	K562	blood:

Variant related genes	Relation type
ENSG00000213639	Chromatin interaction
ENSG00000136143	Chromatin interaction
ENSG00000136156	Chromatin interaction
ENSG00000136146	Chromatin interaction
ENSG00000136159	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1327655	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17350996	0.87[EUR][1000 genomes]
rs2025865	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3949847	0.81[CEU][hapmap]
rs4941627	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4942742	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4942743	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4942747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942748	0.83[EUR][1000 genomes]
rs4942749	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4942750	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4942751	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4942752	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59829900	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6561434	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7317431	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7318704	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7322766	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7323969	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7331551	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7332147	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7332326	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7333237	0.99[ASN][1000 genomes]
rs7333247	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7338844	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7338999	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7339370	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7981114	0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7986400	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285165	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9316346	0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9316347	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9316348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316349	0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9316352	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9316353	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9316354	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9316355	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9316356	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9316357	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9316358	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9316359	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9562800	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9562806	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9562808	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9567993	0.86[EUR][1000 genomes]
rs9567994	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs9567999	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568000	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9568001	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9568002	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9568003	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9568004	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9568005	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9568006	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9568008	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9568009	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9568010	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9568014	0.94[CEU][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes]
rs9591135	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9591138	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9591139	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9591140	0.88[EUR][1000 genomes]
rs9595835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9595836	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9595837	0.81[EUR][1000 genomes]
rs9595843	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9595851	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS 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	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS 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	42 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48666800-48669400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr13:48667000-48669400	Active TSS	K562	blood
3	chr13:48667600-48669400	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr13:48667600-48669600	Active TSS	A549	lung
5	chr13:48667600-48670000	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr13:48667800-48669200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr13:48667800-48669400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr13:48667800-48669400	Active TSS	NHLF	lung
9	chr13:48667800-48669600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr13:48667800-48669600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr13:48667800-48669600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr13:48667800-48669600	Active TSS	Right Atrium	heart
13	chr13:48667800-48669600	Active TSS	Right Ventricle	heart
14	chr13:48668000-48669200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr13:48668000-48669400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr13:48668000-48669400	Active TSS	H1 Cell Line	embryonic stem cell
17	chr13:48668000-48669400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr13:48668000-48669400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr13:48668000-48669400	Active TSS	Fetal Muscle Trunk	muscle
20	chr13:48668000-48669400	Active TSS	HSMMtube	muscle
21	chr13:48668000-48670000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr13:48668200-48669200	Active TSS	Lung	lung
23	chr13:48668200-48669200	Active TSS	Sigmoid Colon	Sigmoid Colon
24	chr13:48668200-48669200	Active TSS	Small Intestine	intestine
25	chr13:48668200-48669200	Active TSS	GM12878-XiMat	blood
26	chr13:48668200-48669400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr13:48668200-48669400	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr13:48668200-48669400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr13:48668200-48669400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr13:48668200-48669400	Active TSS	Fetal Intestine Large	intestine
31	chr13:48668200-48669600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr13:48668200-48669600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr13:48668200-48669600	Active TSS	Aorta	Aorta
34	chr13:48668200-48669600	Active TSS	Left Ventricle	heart
35	chr13:48668200-48669800	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr13:48668400-48669200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
37	chr13:48668400-48669400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr13:48668400-48669400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr13:48668400-48669400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr13:48668400-48669400	Active TSS	Esophagus	oesophagus
41	chr13:48668400-48669400	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr13:48668400-48669400	Active TSS	Fetal Stomach	stomach
43	chr13:48668400-48669400	Active TSS	Gastric	stomach
44	chr13:48668400-48669400	Active TSS	Stomach Mucosa	stomach
45	chr13:48668400-48669400	Active TSS	NHDF-Ad	bronchial
46	chr13:48668400-48669600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr13:48668400-48669600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr13:48668400-48669600	Active TSS	Muscle Satellite Cultured Cells	--
49	chr13:48668400-48669600	Active TSS	Fetal Brain Female	brain
50	chr13:48668400-48669600	Active TSS	Fetal Intestine Small	intestine

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