Variant report

Variant	rs3852063
Chromosome Location	chr3:52349204-52349205
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	chr3:52349193-52349243	Caco-2	colon:	n/a
2	chr3:52349193-52349243	GM12892	blood:	n/a
3	chr3:52349193-52349243	GM12878	blood:	n/a
4	chr3:52349193-52349243	AG04450	lung:	fetal
5	chr3:52349193-52349243	HIPEpiC	eye:	n/a
6	chr3:52349193-52349243	HEEpiC	esophagus:	n/a
7	chr3:52349193-52349243	HAEpiC	amniotic membrane:	n/a
8	chr3:52349193-52349243	AG09309	skin:	n/a
9	chr3:52349193-52349243	Hepatocyte	liver:	n/a
10	chr3:52349193-52349243	GM19239	blood:	n/a
11	chr3:52349193-52349243	AG04449	skin:	fetal
12	chr3:52349193-52349243	HCM	heart:	n/a
13	chr3:52349193-52349243	NT2-D1	testis:	n/a
14	chr3:52349193-52349243	AoSMC	blood vessel:	n/a
15	chr3:52349193-52349243	NHBE	bronchial:	n/a
16	chr3:52349193-52349243	T-47D	breast:	n/a
17	chr3:52349193-52349243	BJ	skin:	n/a
18	chr3:52349193-52349243	AG10803	skin:	n/a
19	chr3:52349193-52349243	HRPEpiC	eye:	n/a
20	chr3:52349193-52349243	HMEC	breast:	n/a
21	chr3:52349193-52349243	LNCaP	prostate:	n/a
22	chr3:52349193-52349243	HPAEpiC	pulmonary alveolar:	n/a
23	chr3:52349193-52349243	HCPEpiC	choroid plexus:	n/a
24	chr3:52349193-52349243	HRE	kidney:	n/a
25	chr3:52349193-52349243	NB4	blood:	n/a
26	chr3:52349193-52349243	MCF10A-Er-Src	breast:	n/a
27	chr3:52349193-52349243	MCF-7	breast:	n/a
28	chr3:52349193-52349243	H1-hESC	embryonic stem cell:	embryo
29	chr3:52349193-52349243	HepG2	liver:	n/a
30	chr3:52349193-52349243	SK-N-SH_RA	brain:	n/a
31	chr3:52349193-52349243	ProgFib	skin:	n/a
32	chr3:52349193-52349243	PFSK-1	brain:	n/a
33	chr3:52349193-52349243	HNPCEpiC	eye:	n/a
34	chr3:52349193-52349243	GM06990	blood:	n/a
35	chr3:52349193-52349243	HRCEpiC	kidney:	n/a
36	chr3:52349193-52349243	SK-N-MC	brain:	n/a
37	chr3:52349193-52349243	NH-A	brain:	n/a
38	chr3:52349193-52349243	HL-60	blood:	n/a
39	chr3:52349193-52349243	HUVEC	blood vessel:	n/a
40	chr3:52349193-52349243	CMK	blood:	n/a
41	chr3:52349193-52349243	HEK293	kidney:	embryo
42	chr3:52349193-52349243	U87	brain:	n/a
43	chr3:52349193-52349243	ovcar-3	ovarian:	n/a
44	chr3:52349193-52349243	BE2_C	brain:	n/a
45	chr3:52349193-52349243	A549	lung:	n/a
46	chr3:52349193-52349243	K562	blood:	n/a
47	chr3:52349193-52349243	AG09319	gingival:	n/a
48	chr3:52349193-52349243	NHDF-neo	bronchial:	n/a
49	chr3:52349193-52349243	IMR90	lung:	fetal
50	chr3:52349193-52349243	PrEC	prostate:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr3:52347614..52350493-chr3:52351552..52354517,2	K562	blood:
2	chr3:52347090..52349395-chr3:52447262..52449654,2	K562	blood:
3	chr3:52336392..52338122-chr3:52347740..52349816,2	K562	blood:
4	chr3:52311115..52314104-chr3:52347391..52350220,2	K562	blood:
5	chr3:52272103..52274162-chr3:52347959..52349801,2	MCF-7	breast:

No data

Variant related genes	Relation type
DNAH1	CpG island
ENSG00000239732	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000164091	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1060330	0.86[ASN][1000 genomes]
rs11717383	0.85[ASN][1000 genomes]
rs13094687	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1546737	0.93[EUR][1000 genomes]
rs2267847	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2272088	0.82[AMR][1000 genomes]
rs2276834	0.88[ASN][1000 genomes]
rs34228726	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34569561	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34656997	0.82[AFR][1000 genomes]
rs353547	0.86[ASN][1000 genomes]
rs3844291	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3852064	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57615517	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57630131	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59565798	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6445358	0.86[ASN][1000 genomes]
rs730050	0.88[ASN][1000 genomes]
rs7614727	0.86[ASN][1000 genomes]
rs7618915	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7622851	0.89[ASN][1000 genomes]
rs7629072	0.86[ASN][1000 genomes]
rs9311474	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
4	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
5	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
6	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
7	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
8	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3852063	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52327200-52351600	Weak transcription	Aorta	Aorta
2	chr3:52327400-52351600	Weak transcription	Brain Anterior Caudate	brain
3	chr3:52328200-52366000	Weak transcription	Brain Angular Gyrus	brain
4	chr3:52328800-52367600	Weak transcription	Brain Substantia Nigra	brain
5	chr3:52329200-52351600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:52333000-52351600	Weak transcription	Thymus	Thymus
8	chr3:52334000-52351400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:52334200-52349600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:52335400-52351400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:52338400-52351400	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:52339800-52351200	Weak transcription	Right Ventricle	heart
13	chr3:52342600-52351200	Weak transcription	Fetal Lung	lung
14	chr3:52342600-52351200	Weak transcription	Pancreas	Pancrea
15	chr3:52343000-52351200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:52343200-52351200	Weak transcription	Gastric	stomach
17	chr3:52343800-52350800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:52344400-52351200	Weak transcription	Ovary	ovary
19	chr3:52344600-52351200	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr3:52344600-52378600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:52344800-52349600	Weak transcription	Liver	Liver
22	chr3:52344800-52351200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:52344800-52351400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:52345200-52351200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:52345200-52351200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:52345400-52351200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:52345400-52351200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:52345600-52351200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr3:52345800-52351200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:52345800-52351200	Weak transcription	Fetal Intestine Large	intestine
31	chr3:52345800-52351600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:52345800-52351600	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:52346000-52349400	Weak transcription	Fetal Brain Female	brain
34	chr3:52346200-52349400	Weak transcription	Brain Germinal Matrix	brain
35	chr3:52346200-52349400	Weak transcription	Fetal Brain Male	brain
36	chr3:52346200-52349600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr3:52346200-52349800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr3:52346200-52351200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr3:52346400-52351400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:52346400-52351400	Weak transcription	Primary T cells from cord blood	blood
41	chr3:52346600-52349400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:52346800-52349400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:52347200-52349400	Enhancers	Esophagus	oesophagus
44	chr3:52347400-52350400	Enhancers	HSMMtube	muscle
45	chr3:52347400-52350600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:52347600-52351200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:52347800-52350200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr3:52347800-52351200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr3:52347800-52351200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:52348000-52351200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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