Variant report

Variant	rs3852064
Chromosome Location	chr3:52349412-52349413
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000239732	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000247596	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1060330	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs11712164	0.82[JPT][hapmap]
rs11717383	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs13094687	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs1546737	1.00[CEU][hapmap];0.92[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs2267847	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2272088	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs2276834	0.87[ASN][1000 genomes]
rs34228726	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34569561	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs353547	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs3844291	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3852063	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs411457	0.81[CHB][hapmap]
rs57615517	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57630131	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58781613	0.87[AFR][1000 genomes]
rs59565798	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs610060	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs61734628	0.82[AFR][1000 genomes]
rs6445358	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs730050	0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs731831	0.90[CEU][hapmap]
rs73838354	0.87[AFR][1000 genomes]
rs7614727	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7618915	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7622851	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7629072	0.85[ASN][1000 genomes]
rs7641255	0.97[LWK][hapmap];1.00[YRI][hapmap]
rs9311474	0.88[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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs3852064	NEK4	cis	cerebellum	SCAN
rs3852064	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs3852064	NEK4	cis	parietal	SCAN
rs3852064	TMEM110	cis	parietal	SCAN
rs3852064	FLJ12442	cis	multi-tissue	Pritchard
rs3852064	ITIH4	cis	multi-tissue	Pritchard
rs3852064	NT5DC2	cis	parietal	SCAN
rs3852064	PRKCD	cis	parietal	SCAN
rs3852064	ITIH3	cis	parietal	SCAN
rs3852064	GNL3	cis	parietal	SCAN
rs3852064	RBM6	cis	cerebellum	SCAN
rs3852064	GLT8D1	cis	lymphoblastoid	seeQTL
rs3852064	ITIH4	cis	cerebellum	SCAN
rs3852064	ITIH4	cis	parietal	SCAN
rs3852064	SPCS1	cis	parietal	SCAN
rs3852064	NT5DC2	cis	lymphoblastoid	seeQTL
rs3852064	GNL3	cis	cerebellum	SCAN
rs3852064	CACNA2D3	cis	parietal	SCAN

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	chr3:52346200-52349600	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr3:52346200-52349800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:52346200-52351200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr3:52346400-52351400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:52346400-52351400	Weak transcription	Primary T cells from cord blood	blood
38	chr3:52347400-52350400	Enhancers	HSMMtube	muscle
39	chr3:52347400-52350600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:52347600-52351200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:52347800-52350200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr3:52347800-52351200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:52347800-52351200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr3:52348000-52351200	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:52348000-52351200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:52348000-52351600	Weak transcription	NHLF	lung
47	chr3:52348000-52353600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:52348200-52351000	Strong transcription	Fetal Intestine Small	intestine
49	chr3:52348200-52351200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:52348200-52351200	Weak transcription	Rectal Mucosa Donor 29	rectum

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