Variant report

Variant	rs3733082
Chromosome Location	chr3:53914093-53914094
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:53914075-53914125	HRPEpiC	eye:	n/a
2	chr3:53914075-53914125	H1-hESC	embryonic stem cell:	embryo
3	chr3:53914075-53914125	NB4	blood:	n/a
4	chr3:53914075-53914125	SKMC	muscle:	n/a
5	chr3:53914075-53914125	IMR90	lung:	fetal
6	chr3:53914075-53914125	AG04449	skin:	fetal
7	chr3:53914075-53914125	Jurkat	blood:	n/a
8	chr3:53914075-53914125	AoSMC	blood vessel:	n/a
9	chr3:53914075-53914125	Caco-2	colon:	n/a
10	chr3:53914075-53914125	NH-A	brain:	n/a
11	chr3:53914075-53914125	NHDF-neo	bronchial:	n/a
12	chr3:53914075-53914125	PrEC	prostate:	n/a
13	chr3:53914075-53914125	U87	brain:	n/a
14	chr3:53914075-53914125	Hela-S3	cervix:	n/a
15	chr3:53914075-53914125	AG10803	skin:	n/a
16	chr3:53914075-53914125	SAEC	small airway:	n/a
17	chr3:53914075-53914125	PFSK-1	brain:	n/a
18	chr3:53914075-53914125	HRE	kidney:	n/a
19	chr3:53914075-53914125	MCF-7	breast:	n/a
20	chr3:53914075-53914125	HRCEpiC	kidney:	n/a
21	chr3:53914075-53914125	LNCaP	prostate:	n/a
22	chr3:53914075-53914125	SK-N-SH	brain:	n/a
23	chr3:53914075-53914125	CMK	blood:	n/a
24	chr3:53914075-53914125	PANC-1	pancreas:	n/a
25	chr3:53914075-53914125	HCPEpiC	choroid plexus:	n/a
26	chr3:53914075-53914125	SK-N-SH_RA	brain:	n/a
27	chr3:53914075-53914125	BE2_C	brain:	n/a
28	chr3:53914075-53914125	NT2-D1	testis:	n/a
29	chr3:53914075-53914125	HEEpiC	esophagus:	n/a
30	chr3:53914075-53914125	HEK293	kidney:	embryo
31	chr3:53914075-53914125	GM12892	blood:	n/a
32	chr3:53914075-53914125	AG09309	skin:	n/a
33	chr3:53914075-53914125	A549	lung:	n/a
34	chr3:53914075-53914125	GM06990	blood:	n/a
35	chr3:53914075-53914125	BJ	skin:	n/a
36	chr3:53914075-53914125	HepG2	liver:	n/a
37	chr3:53914075-53914125	HUVEC	blood vessel:	n/a
38	chr3:53914075-53914125	ovcar-3	ovarian:	n/a
39	chr3:53914075-53914125	MCF10A-Er-Src	breast:	n/a
40	chr3:53914075-53914125	NHBE	bronchial:	n/a
41	chr3:53914075-53914125	RPTEC	kidney:	n/a
42	chr3:53914075-53914125	HMEC	breast:	n/a
43	chr3:53914075-53914125	ProgFib	skin:	n/a
44	chr3:53914075-53914125	HNPCEpiC	eye:	n/a
45	chr3:53914075-53914125	GM19239	blood:	n/a
46	chr3:53914075-53914125	GM12891	blood:	n/a
47	chr3:53914075-53914125	HAEpiC	amniotic membrane:	n/a
48	chr3:53914075-53914125	ECC-1	luminal epithelium:	n/a
49	chr3:53914075-53914125	HPAEpiC	pulmonary alveolar:	n/a
50	chr3:53914075-53914125	HCT-116	colon:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:53908420..53912131-chr3:53913956..53917012,3	MCF-7	breast:
2	chr3:53913333..53919757-chr3:53920203..53928086,26	K562	blood:
3	chr3:53906924..53910795-chr3:53914021..53916121,3	MCF-7	breast:
4	chr3:53913820..53918433-chr3:53924406..53927799,6	MCF-7	breast:
5	chr3:53901391..53905529-chr3:53913413..53917026,5	MCF-7	breast:

No data

Variant related genes	Relation type
ACTR8	CpG island
ENSG00000113812	Chromatin interaction
ENSG00000113811	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11714234	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717931	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11718358	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12496534	0.90[ASN][1000 genomes]
rs2276842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28374298	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28715733	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774626	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687593	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687596	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4687754	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.87[TSI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687759	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55835925	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56708826	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs57777269	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs726028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs744381	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611432	0.90[ASN][1000 genomes]
rs7628619	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636572	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646455	0.92[AFR][1000 genomes];1.00[EUR][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1014752	chr3:53912429-54123246	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53888400-53914600	Weak transcription	Stomach Mucosa	stomach
2	chr3:53890800-53914600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:53891000-53914200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:53891000-53914200	Strong transcription	Duodenum Mucosa	Duodenum
5	chr3:53891400-53914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:53892000-53914400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:53892200-53914400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:53892200-53914600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:53892400-53914200	Strong transcription	Stomach Smooth Muscle	stomach
10	chr3:53892400-53914400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:53892600-53914200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:53892600-53914400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:53892600-53914400	Strong transcription	Fetal Muscle Leg	muscle
14	chr3:53892800-53914200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:53892800-53914200	Strong transcription	Fetal Muscle Trunk	muscle
16	chr3:53892800-53914200	Strong transcription	Thymus	Thymus
17	chr3:53892800-53914400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:53892800-53914600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr3:53893000-53914400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:53893200-53914200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:53893200-53914200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:53893200-53914200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:53893200-53914600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:53893400-53914200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:53894200-53914400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:53894400-53914400	Strong transcription	Fetal Thymus	thymus
27	chr3:53894800-53914200	Strong transcription	Primary hematopoietic stem cells	blood
28	chr3:53894800-53914200	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr3:53895000-53914200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:53895000-53914400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:53895200-53914200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr3:53895200-53914200	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:53895200-53914200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:53895600-53914200	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr3:53896800-53914200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:53897200-53914200	Strong transcription	Osteobl	bone
37	chr3:53897800-53914200	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:53898600-53914200	Strong transcription	HMEC	breast
39	chr3:53898600-53914400	Strong transcription	Dnd41	blood
40	chr3:53898800-53914200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr3:53898800-53914200	Strong transcription	NH-A	brain
42	chr3:53899800-53914200	Strong transcription	NHDF-Ad	bronchial
43	chr3:53901000-53914200	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr3:53901000-53914200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:53901000-53914200	Strong transcription	Brain Cingulate Gyrus	brain
46	chr3:53901000-53914400	Strong transcription	HSMM	muscle
47	chr3:53901400-53914200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:53901400-53914200	Strong transcription	Liver	Liver
49	chr3:53901400-53914200	Strong transcription	Hela-S3	cervix
50	chr3:53901600-53914200	Strong transcription	Brain Substantia Nigra	brain

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