Variant report

Variant	rs4960009
Chromosome Location	chr6:4602450-4602451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPP40-3	chr6:4602411-4602654	ENSG00000260673.1
2	lnc-RPP40-3	chr6:4602239-4602631	NONHSAT107457
3	lnc-RPP40-3	chr6:4602414-4602654	NONHSAT107456

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11751457	0.92[EUR][1000 genomes]
rs11756102	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11962754	0.94[EUR][1000 genomes]
rs11964426	1.00[CEU][hapmap]
rs11964427	0.91[EUR][1000 genomes]
rs17138534	0.94[EUR][1000 genomes]
rs17138543	0.81[EUR][1000 genomes]
rs2235724	0.94[EUR][1000 genomes]
rs377207	0.91[EUR][1000 genomes]
rs378901	0.88[EUR][1000 genomes]
rs385236	0.91[EUR][1000 genomes]
rs385884	0.91[EUR][1000 genomes]
rs390126	0.91[EUR][1000 genomes]
rs390617	0.86[EUR][1000 genomes]
rs400405	0.83[EUR][1000 genomes]
rs413716	0.91[EUR][1000 genomes]
rs418563	0.91[EUR][1000 genomes]
rs421930	0.91[EUR][1000 genomes]
rs424137	0.91[EUR][1000 genomes]
rs438021	0.86[EUR][1000 genomes]
rs453768	0.91[EUR][1000 genomes]
rs4960004	0.91[EUR][1000 genomes]
rs601192	0.91[EUR][1000 genomes]
rs62384944	0.95[EUR][1000 genomes]
rs6911463	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs6912325	0.91[EUR][1000 genomes]
rs6913171	0.91[EUR][1000 genomes]
rs9328262	0.94[EUR][1000 genomes]
rs9502199	0.91[EUR][1000 genomes]
rs9502200	0.91[EUR][1000 genomes]
rs9502206	0.95[EUR][1000 genomes]
rs9504151	0.91[EUR][1000 genomes]
rs9504156	0.94[EUR][1000 genomes]
rs9504159	0.95[EUR][1000 genomes]
rs9504163	0.95[EUR][1000 genomes]
rs9504165	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9504166	0.99[EUR][1000 genomes]
rs9504168	0.88[EUR][1000 genomes]
rs9504169	0.86[EUR][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	esv3421990	chr6:4446933-4659639	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830576	chr6:4447554-4610604	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	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
4	nsv883415	chr6:4546491-4629654	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4599800-4604000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:4599800-4604400	Enhancers	NHEK	skin
3	chr6:4600000-4604400	Enhancers	HMEC	breast
4	chr6:4600000-4606800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:4600400-4604400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:4601000-4607000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:4601200-4603000	Weak transcription	HSMMtube	muscle
8	chr6:4601200-4603200	Weak transcription	Fetal Heart	heart
9	chr6:4601200-4603200	Weak transcription	NHDF-Ad	bronchial
10	chr6:4601200-4603200	Weak transcription	Osteobl	bone
11	chr6:4601200-4606400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:4601200-4606400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:4601200-4606400	Weak transcription	Right Ventricle	heart
14	chr6:4601400-4602800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:4601400-4603000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:4601400-4603000	Weak transcription	Esophagus	oesophagus
17	chr6:4601400-4603000	Weak transcription	NH-A	brain
18	chr6:4601400-4603800	Weak transcription	HUVEC	blood vessel
19	chr6:4601400-4607000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:4601600-4602800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:4601600-4606000	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:4601600-4606800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:4601800-4603000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:4601800-4603000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:4601800-4603000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:4601800-4604000	Enhancers	Placenta Amnion	Placenta Amnion
27	chr6:4601800-4607000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:4602000-4602600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:4602000-4603000	Weak transcription	HSMM	muscle
30	chr6:4602000-4603000	Weak transcription	NHLF	lung
31	chr6:4602200-4603000	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr6:4602200-4603200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:4602400-4602800	Enhancers	Spleen	Spleen
34	chr6:4602400-4604400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr6:4602400-4604400	Enhancers	Placenta	Placenta

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