Variant report

Variant	rs1448434
Chromosome Location	chr3:119043011-119043012
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr3:119042372-119044133	IMR90	lung:	n/a	chr3:119043880-119043889
2	MTA3	chr3:119040824-119043149	GM12878	blood:	n/a	n/a
3	PML	chr3:119040990-119043120	GM12878	blood:	n/a	n/a
4	CEBPB	chr3:119041662-119043052	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:119040990-119043033	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119040381..119043387-chr3:119393976..119396207,3	K562	blood:
2	chr3:119016211..119028042-chr3:119037960..119043695,12	MCF-7	breast:
3	chr3:119041713..119043287-chr3:119530571..119533210,2	MCF-7	breast:
4	chr3:119012312..119014941-chr3:119040203..119043471,4	MCF-7	breast:
5	chr3:119011662..119015799-chr3:119040784..119043293,4	MCF-7	breast:
6	chr3:119041710..119043371-chr3:119051543..119054199,2	K562	blood:
7	chr3:119040625..119043456-chr3:119181021..119182647,3	MCF-7	breast:
8	chr3:119040520..119043561-chr3:119060040..119062334,3	MCF-7	breast:

No data

Variant related genes	Relation type
ARHGAP31	TF binding region
ARHGAP31-AS1	TF binding region
ENSG00000242829	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000138495	Chromatin interaction
ENSG00000207310	Chromatin interaction
ENSG00000031081	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10511386	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934490	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12497738	0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13314464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1375135	0.96[CEU][hapmap];0.89[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2044621	0.96[YRI][hapmap]
rs2278781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732412	0.92[CEU][hapmap]
rs4687994	0.96[CEU][hapmap];0.82[GIH][hapmap];0.80[MEX][hapmap];0.87[EUR][1000 genomes]
rs58568360	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62265236	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62265237	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6438518	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6438519	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6438520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438522	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6438523	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762580	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6785727	0.96[CEU][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6786522	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6789881	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6799733	1.00[CEU][hapmap];0.88[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7610546	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7611832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619210	0.86[EUR][1000 genomes]
rs7644570	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7649480	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7649930	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9822211	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9825078	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9834750	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9847963	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9861372	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9861688	1.00[CEU][hapmap];0.89[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9863675	0.85[LWK][hapmap];0.96[YRI][hapmap]
rs9877740	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1448434	GTF2E1	cis	cerebellum	SCAN
rs1448434	CCDC14	cis	parietal	SCAN
rs1448434	MYO10	trans	parietal	SCAN
rs1448434	KPNA1	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119042000-119043200	Enhancers	Fetal Heart	heart
2	chr3:119042600-119043200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr3:119042600-119043200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:119042600-119043200	Enhancers	Lung	lung
5	chr3:119042600-119043600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:119042600-119043800	Weak transcription	Osteobl	bone
7	chr3:119042600-119044400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:119042600-119044400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
9	chr3:119042600-119045200	Weak transcription	Brain Substantia Nigra	brain
10	chr3:119042600-119047200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:119042600-119047800	Weak transcription	Ovary	ovary
12	chr3:119042600-119048000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:119042600-119048000	Weak transcription	Brain Angular Gyrus	brain
14	chr3:119042600-119048000	Weak transcription	NH-A	brain
15	chr3:119042600-119048200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:119042600-119048400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:119042600-119048400	Weak transcription	Aorta	Aorta
18	chr3:119042600-119048600	Weak transcription	HSMM	muscle
19	chr3:119042600-119050000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:119042600-119050200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:119042600-119050400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:119042600-119050400	Weak transcription	HSMMtube	muscle
23	chr3:119042600-119050400	Weak transcription	NHEK	skin
24	chr3:119042600-119054000	Weak transcription	NHLF	lung
25	chr3:119042600-119055600	Weak transcription	Fetal Brain Male	brain
26	chr3:119042800-119043200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:119042800-119043200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
28	chr3:119042800-119043200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr3:119042800-119043200	Enhancers	Primary B cells from peripheral blood	blood
30	chr3:119042800-119043200	Enhancers	Primary T cells fromperipheralblood	blood
31	chr3:119042800-119043200	Enhancers	Primary hematopoietic stem cells	blood
32	chr3:119042800-119043200	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr3:119042800-119043200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr3:119042800-119043200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:119042800-119043200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr3:119042800-119043200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:119042800-119043200	Enhancers	Brain Anterior Caudate	brain
38	chr3:119042800-119043800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:119042800-119044000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:119042800-119044000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:119042800-119044400	Enhancers	H1 Cell Line	embryonic stem cell
42	chr3:119042800-119044400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr3:119042800-119044400	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr3:119042800-119044400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:119042800-119045200	Weak transcription	Placenta	Placenta
46	chr3:119042800-119045400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:119042800-119045600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:119042800-119046600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:119042800-119047000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr3:119042800-119048000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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