Variant report

Variant	rs9378411
Chromosome Location	chr6:4734465-4734466
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4733687..4736234-chr6:4773695..4776537,2	K562	blood:
2	chr6:4733392..4734998-chr6:4742508..4744758,2	MCF-7	breast:
3	chr6:4733801..4736473-chr6:4737548..4740491,3	K562	blood:
4	chr6:4732911..4734620-chr6:4774132..4776554,2	MCF-7	breast:
5	chr6:4730542..4732664-chr6:4733935..4736268,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPP40-7	chr6:4734457-4734611	NONHSAT107486

Variant related genes	Relation type
ENSG00000236336	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10458178	0.95[ASN][1000 genomes]
rs11242974	0.95[ASN][1000 genomes]
rs11242977	0.95[ASN][1000 genomes]
rs11242978	0.95[ASN][1000 genomes]
rs11755832	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11759784	0.95[ASN][1000 genomes]
rs12196896	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12208133	0.95[ASN][1000 genomes]
rs12211355	0.95[ASN][1000 genomes]
rs12214737	0.97[ASN][1000 genomes]
rs35640627	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35836829	0.95[ASN][1000 genomes]
rs4960042	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6597094	0.95[ASN][1000 genomes]
rs6597095	0.94[ASN][1000 genomes]
rs6915353	0.95[ASN][1000 genomes]
rs6917691	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6931290	0.97[ASN][1000 genomes]
rs6931832	0.85[CHB][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs6932591	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6937790	0.85[CHB][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs6938514	0.97[ASN][1000 genomes]
rs6941511	0.95[ASN][1000 genomes]
rs6941562	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7745237	0.95[ASN][1000 genomes]
rs7748184	0.95[ASN][1000 genomes]
rs7748335	0.95[ASN][1000 genomes]
rs7748862	0.95[ASN][1000 genomes]
rs7762773	0.95[ASN][1000 genomes]
rs7762927	0.95[ASN][1000 genomes]
rs7767658	0.95[ASN][1000 genomes]
rs7767968	0.95[ASN][1000 genomes]
rs907841	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9328271	0.95[ASN][1000 genomes]
rs9328272	0.85[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9328273	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9328274	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9378409	0.95[ASN][1000 genomes]
rs9378410	0.95[ASN][1000 genomes]
rs9378906	0.94[ASN][1000 genomes]
rs9378907	0.95[ASN][1000 genomes]
rs9378908	0.95[ASN][1000 genomes]
rs9378909	0.95[ASN][1000 genomes]
rs9378910	0.85[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9392062	0.95[ASN][1000 genomes]
rs9392064	0.95[ASN][1000 genomes]
rs9392626	0.95[ASN][1000 genomes]
rs9392628	0.95[ASN][1000 genomes]
rs9392629	0.95[ASN][1000 genomes]
rs9392630	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9392631	0.85[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9392632	0.85[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9392634	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9392635	0.85[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9405764	0.95[ASN][1000 genomes]
rs9405765	0.95[ASN][1000 genomes]
rs9405766	0.95[ASN][1000 genomes]
rs9405767	0.95[ASN][1000 genomes]
rs9405768	0.95[ASN][1000 genomes]
rs9405769	0.95[ASN][1000 genomes]
rs9405770	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9405771	0.85[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9405772	0.85[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9405773	0.85[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9405774	0.84[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9405776	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9504222	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv3429586	chr6:4719363-4792438	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1017938	chr6:4729592-4774914	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4732400-4735400	Enhancers	Placenta Amnion	Placenta Amnion
2	chr6:4732800-4735200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:4732800-4735200	Enhancers	Placenta	Placenta
4	chr6:4733200-4735200	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr6:4733400-4734600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr6:4733400-4735000	Enhancers	HSMM	muscle
7	chr6:4733400-4735200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr6:4733400-4735200	Enhancers	Colon Smooth Muscle	Colon
9	chr6:4733400-4735200	Enhancers	HUVEC	blood vessel
10	chr6:4733400-4735200	Enhancers	K562	blood
11	chr6:4733600-4734600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:4733600-4734600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:4733600-4734600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:4733600-4734600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:4733600-4734600	Enhancers	NH-A	brain
16	chr6:4733600-4735000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:4733600-4735200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:4733600-4735200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:4733600-4735200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:4733600-4735200	Enhancers	NHDF-Ad	bronchial
21	chr6:4733600-4735200	Enhancers	Osteobl	bone
22	chr6:4733600-4743000	Weak transcription	Right Atrium	heart
23	chr6:4734000-4735000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:4734000-4735000	Enhancers	Fetal Muscle Trunk	muscle
25	chr6:4734000-4735200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:4734000-4735200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:4734000-4735200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:4734000-4735200	Enhancers	HMEC	breast
29	chr6:4734000-4735200	Enhancers	NHLF	lung
30	chr6:4734000-4740600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr6:4734200-4735200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr6:4734200-4735200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:4734200-4735200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:4734200-4735200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:4734200-4735200	Enhancers	Fetal Muscle Leg	muscle
36	chr6:4734200-4735200	Enhancers	HSMMtube	muscle
37	chr6:4734400-4734600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:4734400-4734600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr6:4734400-4734600	Bivalent Enhancer	Adipose Nuclei	Adipose
40	chr6:4734400-4734600	Flanking Active TSS	NHEK	skin
41	chr6:4734400-4734800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr6:4734400-4734800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:4734400-4734800	Enhancers	Esophagus	oesophagus
44	chr6:4734400-4734800	Active TSS	A549	lung
45	chr6:4734400-4735000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr6:4734400-4735000	Flanking Active TSS	Hela-S3	cervix
47	chr6:4734400-4735400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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