Variant report

Variant	rs7652667
Chromosome Location	chr3:52866535-52866536
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52864085..52867017-chr3:52872869..52875445,2	MCF-7	breast:
2	chr3:52803948..52806345-chr3:52865313..52866850,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248592	Chromatin interaction
ENSG00000213533	Chromatin interaction
ENSG00000114904	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs11715347	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719137	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11915546	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11918800	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11922961	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239548	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240915	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240917	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2245538	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2245647	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2256332	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276823	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2336558	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2535633	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774364	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56019197	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60332615	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6445541	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6769789	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7612624	0.82[ASN][1000 genomes]
rs7617468	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7620690	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7630552	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7652667	GNL3	cis	cerebellum	SCAN
rs7652667	GLYCTK	cis	parietal	SCAN
rs7652667	SEMA3G	cis	parietal	SCAN
rs7652667	ITIH4	cis	lymphoblastoid	seeQTL
rs7652667	ITIH4-AS1	cis	lung	GTEx
rs7652667	ITIH4	cis	cerebellum	SCAN
rs7652667	WDR6	cis	cerebellum	SCAN
rs7652667	RFT1	cis	cerebellum	SCAN
rs7652667	ITIH4-AS1	cis	Artery Tibial	GTEx
rs7652667	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs7652667	TEX264	cis	parietal	SCAN
rs7652667	ITIH4-AS1	cis	Artery Aorta	GTEx
rs7652667	GNL3	cis	parietal	SCAN
rs7652667	ITIH4-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52850200-52868400	Weak transcription	Colonic Mucosa	Colon
2	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
4	chr3:52853000-52868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:52854800-52869200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
9	chr3:52856400-52868200	Weak transcription	Fetal Lung	lung
10	chr3:52857000-52868600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:52858000-52867800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:52858000-52868400	Weak transcription	Brain Germinal Matrix	brain
13	chr3:52858400-52866800	Weak transcription	Fetal Brain Female	brain
14	chr3:52858400-52867200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:52858400-52867600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:52858600-52866800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr3:52858600-52867000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr3:52858800-52866800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:52858800-52868800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:52858800-52868800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:52858800-52869200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:52859400-52869000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:52860200-52869000	Weak transcription	Fetal Intestine Small	intestine
24	chr3:52861200-52868800	Weak transcription	Lung	lung
25	chr3:52862000-52869200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:52863200-52872600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:52864400-52866600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:52864400-52866600	Enhancers	NHLF	lung
30	chr3:52864400-52867200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:52864600-52866600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr3:52864600-52866800	Enhancers	HSMMtube	muscle
34	chr3:52864600-52867000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:52864600-52867400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:52864800-52866600	Enhancers	Aorta	Aorta
37	chr3:52864800-52866600	Enhancers	HSMM	muscle
38	chr3:52864800-52867000	Weak transcription	Thymus	Thymus
39	chr3:52865000-52866600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr3:52865000-52866600	Enhancers	NHDF-Ad	bronchial
41	chr3:52865000-52866800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr3:52865000-52867200	Genic enhancers	Fetal Muscle Leg	muscle
43	chr3:52865000-52867800	Enhancers	Psoas Muscle	Psoas
44	chr3:52865000-52869400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:52865200-52867000	Enhancers	Pancreas	Pancrea
46	chr3:52865200-52869000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:52865400-52866600	Enhancers	Adipose Nuclei	Adipose
48	chr3:52865400-52866600	Enhancers	Brain Substantia Nigra	brain
49	chr3:52865600-52866600	Enhancers	Brain Hippocampus Middle	brain
50	chr3:52865600-52867600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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