Variant report

Variant	rs6462932
Chromosome Location	chr7:39607399-39607400
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:39604710..39608797-chr7:39663149..39665225,4	K562	blood:
2	chr7:39605618..39607861-chr7:39772706..39774759,2	K562	blood:
3	chr7:39605969..39608430-chr7:39663149..39665540,3	K562	blood:
4	chr7:39606078..39608053-chr7:39609216..39613025,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006451	Chromatin interaction
ENSG00000188185	Chromatin interaction
ENSG00000241127	Chromatin interaction
ENSG00000236015	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10274595	0.86[ASN][1000 genomes]
rs12112104	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12531635	0.89[ASN][1000 genomes]
rs12701746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2329453	0.99[ASN][1000 genomes]
rs4720327	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4720328	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4723876	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.94[ASN][1000 genomes]
rs56211944	0.86[ASN][1000 genomes]
rs62453607	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62453608	0.92[ASN][1000 genomes]
rs6943186	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7808493	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.92[YRI][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021180	chr7:39424988-39642261	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1026951	chr7:39429036-39642261	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1018430	chr7:39455497-39643569	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv970467	chr7:39605971-39615006	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6462932	VPS41	cis	parietal	SCAN
rs6462932	GPR141	cis	parietal	SCAN
rs6462932	RALA	cis	cerebellum	SCAN
rs6462932	PSMA2	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39605000-39607400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:39605000-39607600	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr7:39605000-39607600	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr7:39605000-39607600	Active TSS	A549	lung
5	chr7:39605000-39607600	Active TSS	NHLF	lung
6	chr7:39605200-39607400	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr7:39605400-39607400	Active TSS	HSMMtube	muscle
8	chr7:39605400-39607600	Active TSS	NH-A	brain
9	chr7:39606400-39607400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr7:39606400-39614000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:39606600-39607400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:39606600-39607400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
13	chr7:39606600-39607400	Flanking Active TSS	Fetal Brain Female	brain
14	chr7:39606600-39607600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:39606600-39607600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:39606600-39607600	Enhancers	Placenta Amnion	Placenta Amnion
17	chr7:39606600-39607600	Flanking Active TSS	Dnd41	blood
18	chr7:39606600-39609000	Weak transcription	Esophagus	oesophagus
19	chr7:39606600-39616200	Weak transcription	Spleen	Spleen
20	chr7:39606600-39616600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:39606600-39616800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:39606600-39618600	Weak transcription	Gastric	stomach
23	chr7:39606600-39619800	Weak transcription	Lung	lung
24	chr7:39606800-39607400	Flanking Active TSS	HepG2	liver
25	chr7:39606800-39607400	Flanking Active TSS	Osteobl	bone
26	chr7:39606800-39607600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr7:39606800-39607600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr7:39606800-39607600	Enhancers	Fetal Brain Male	brain
29	chr7:39606800-39607600	Flanking Active TSS	HMEC	breast
30	chr7:39607000-39607400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr7:39607000-39607400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr7:39607000-39607400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr7:39607000-39607400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr7:39607000-39607400	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr7:39607000-39607600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr7:39607000-39607600	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr7:39607000-39607600	Enhancers	Adipose Nuclei	Adipose
38	chr7:39607000-39607600	Enhancers	Brain Substantia Nigra	brain
39	chr7:39607000-39609200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr7:39607000-39609200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr7:39607000-39609200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr7:39607000-39609800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr7:39607000-39611400	Weak transcription	Left Ventricle	heart
44	chr7:39607000-39616800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr7:39607000-39618800	Weak transcription	Right Ventricle	heart
46	chr7:39607000-39619800	Weak transcription	Ovary	ovary
47	chr7:39607000-39623800	Weak transcription	Pancreas	Pancrea
48	chr7:39607000-39631400	Weak transcription	Aorta	Aorta
49	chr7:39607200-39607400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr7:39607200-39607400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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