Variant report

Variant	rs6445358
Chromosome Location	chr3:52308845-52308846
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52028423..52029953-chr3:52307587..52309359,2	MCF-7	breast:
2	chr3:52273103..52274845-chr3:52307550..52309126,2	K562	blood:
3	chr3:52266609..52268371-chr3:52308578..52311025,2	MCF-7	breast:
4	chr3:52282752..52284466-chr3:52308122..52311758,3	K562	blood:

Variant related genes	Relation type
ENSG00000162244	Chromatin interaction
ENSG00000239732	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000164088	Chromatin interaction
ENSG00000243224	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1060330	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1077142	0.93[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap]
rs11705963	0.83[AFR][1000 genomes]
rs11706108	0.83[AFR][1000 genomes]
rs11717383	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13091545	0.93[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs13094687	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs164640	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs181274	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs187084	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs2272088	0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs2276834	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34228726	0.86[ASN][1000 genomes]
rs34569561	0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs352139	0.81[CHB][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap]
rs352140	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs352158	0.81[CHB][hapmap]
rs352162	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs352163	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs352165	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs352166	0.81[CHB][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap]
rs352167	0.81[CHB][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap]
rs352168	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs352169	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs352170	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs352171	0.81[CHB][hapmap]
rs353547	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs35860312	0.93[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs3844291	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs3852063	0.86[ASN][1000 genomes]
rs3852064	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs411457	0.86[CHB][hapmap]
rs498946	0.91[LWK][hapmap];0.86[MKK][hapmap];0.87[YRI][hapmap]
rs524986	0.81[CHB][hapmap]
rs57615517	0.86[ASN][1000 genomes]
rs57630131	0.82[ASN][1000 genomes]
rs59565798	0.87[ASN][1000 genomes]
rs610060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs614288	0.81[CHB][hapmap]
rs648514	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs66462821	0.81[AFR][1000 genomes]
rs6794675	0.83[AFR][1000 genomes]
rs730050	0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.93[ASN][1000 genomes]
rs7614727	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618915	0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7622851	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7629072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643570	0.93[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs9311474	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	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	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	nsv822090	chr3:52292814-52311153	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs6445358	RBM6	cis	cerebellum	SCAN
rs6445358	GNL3	cis	parietal	SCAN
rs6445358	SEMA3G	cis	cerebellum	SCAN
rs6445358	RBM6	cis	parietal	SCAN
rs6445358	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs6445358	CACNA2D3	cis	parietal	SCAN
rs6445358	DNAH1	cis	cerebellum	SCAN
rs6445358	SPCS1	cis	parietal	SCAN
rs6445358	NDUFAF3	cis	parietal	SCAN
rs6445358	GNL3	cis	cerebellum	SCAN
rs6445358	ITIH4	cis	parietal	SCAN
rs6445358	GLYCTK	cis	parietal	SCAN
rs6445358	NT5DC2	cis	lymphoblastoid	seeQTL
rs6445358	GLYCTK	cis	multi-tissue	Pritchard
rs6445358	GLT8D1	cis	lymphoblastoid	seeQTL
rs6445358	NEK4	cis	parietal	SCAN
rs6445358	NEK4	cis	cerebellum	SCAN
rs6445358	SEMA3G	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52282200-52310000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:52282400-52309600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:52283800-52309600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:52292400-52309400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:52297400-52311200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:52300000-52310200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:52300000-52310200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:52300200-52310200	Weak transcription	HSMMtube	muscle
9	chr3:52300600-52310800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:52301200-52311400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:52302600-52310000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:52302800-52310200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:52303000-52311200	Weak transcription	Esophagus	oesophagus
14	chr3:52303400-52310000	Weak transcription	Aorta	Aorta
15	chr3:52303600-52309600	Genic enhancers	Primary B cells from cord blood	blood
16	chr3:52303800-52309600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:52304000-52311000	Genic enhancers	Primary B cells from peripheral blood	blood
18	chr3:52304200-52309800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:52304400-52310200	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr3:52304800-52309800	Genic enhancers	Dnd41	blood
21	chr3:52305000-52310000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:52305000-52310400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:52305200-52310400	Genic enhancers	Fetal Thymus	thymus
24	chr3:52305600-52309400	Weak transcription	Fetal Kidney	kidney
25	chr3:52305600-52310000	Genic enhancers	HepG2	liver
26	chr3:52305800-52310200	Genic enhancers	Fetal Muscle Leg	muscle
27	chr3:52305800-52310200	Genic enhancers	Monocytes-CD14+_RO01746	blood
28	chr3:52306000-52309400	Weak transcription	Brain Angular Gyrus	brain
29	chr3:52306000-52310000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:52306200-52309400	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:52306200-52309400	Weak transcription	Fetal Brain Male	brain
32	chr3:52306200-52309400	Weak transcription	NHLF	lung
33	chr3:52306200-52309400	Weak transcription	Osteobl	bone
34	chr3:52306200-52309800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:52306400-52309000	Genic enhancers	Muscle Satellite Cultured Cells	--
36	chr3:52306400-52309200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr3:52306600-52309000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr3:52306600-52309600	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr3:52306600-52310800	Weak transcription	Lung	lung
40	chr3:52306800-52309000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:52306800-52309400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
42	chr3:52306800-52309600	Genic enhancers	HUVEC	blood vessel
43	chr3:52307000-52309000	Genic enhancers	Rectal Mucosa Donor 29	rectum
44	chr3:52307000-52309200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:52307000-52309200	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr3:52307000-52309400	Enhancers	Psoas Muscle	Psoas
47	chr3:52307000-52310400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr3:52307000-52311600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr3:52307200-52309600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:52307200-52309800	Enhancers	Left Ventricle	heart

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