Variant report

Variant	rs1856117
Chromosome Location	chr6:114661702-114661703
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:114655643..114657954-chr6:114659786..114662441,2	MCF-7	breast:
2	chr6:114649750..114652393-chr6:114660121..114661764,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MARCKS-5	chr6:114661686-114661779	ENSG00000228624
2	lnc-MARCKS-5	chr6:114661686-114661902	ENSG00000228624

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10080647	0.81[YRI][hapmap]
rs10155706	1.00[AMR][1000 genomes]
rs2031139	0.89[AFR][1000 genomes]
rs2065933	0.89[AFR][1000 genomes]
rs2786206	0.98[AFR][1000 genomes]
rs57078191	0.87[AFR][1000 genomes]
rs57397327	0.89[AFR][1000 genomes]
rs60232257	0.90[AFR][1000 genomes]
rs60233932	0.85[AFR][1000 genomes]
rs61602782	0.89[AFR][1000 genomes]
rs6900066	0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs6932472	0.90[AFR][1000 genomes]
rs73767409	0.88[AFR][1000 genomes]
rs73767452	0.90[AFR][1000 genomes]
rs73767454	0.89[AFR][1000 genomes]
rs73769206	0.83[AFR][1000 genomes]
rs785134	0.89[AFR][1000 genomes]
rs785140	0.92[AFR][1000 genomes]
rs785141	0.93[AFR][1000 genomes]
rs945786	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs9481441	0.84[AFR][1000 genomes]
rs9481448	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9488372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9488374	0.90[AFR][1000 genomes]
rs9488377	0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs9488381	0.83[AFR][1000 genomes]
rs9488382	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9488385	0.83[AFR][1000 genomes]
rs9488386	0.83[AFR][1000 genomes]
rs9488387	0.82[AFR][1000 genomes]
rs9488398	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024062	chr6:114311029-114679557	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
2	esv34434	chr6:114465305-115462799	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv464024	chr6:114489321-114837181	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv604544	chr6:114489321-114837181	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv3692910	chr6:114597419-115480580	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv528128	chr6:114597657-115471129	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv818451	chr6:114597657-115471129	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114659800-114665400	Active TSS	H1 Cell Line	embryonic stem cell
2	chr6:114660400-114662000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr6:114660600-114661800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr6:114660600-114662400	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr6:114660600-114662600	Active TSS	Fetal Brain Female	brain
6	chr6:114660800-114661800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:114660800-114661800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr6:114660800-114661800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:114660800-114662000	Enhancers	Brain Cingulate Gyrus	brain
10	chr6:114661000-114661800	Enhancers	HSMM	muscle
11	chr6:114661000-114662400	Active TSS	HepG2	liver
12	chr6:114661000-114665000	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr6:114661000-114665200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:114661000-114665800	Active TSS	Brain Anterior Caudate	brain
15	chr6:114661200-114661800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:114661200-114662000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:114661200-114662200	Weak transcription	Brain Germinal Matrix	brain
18	chr6:114661200-114662400	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr6:114661200-114662400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:114661200-114665000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:114661200-114665200	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr6:114661400-114662000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr6:114661400-114662200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:114661400-114662200	Weak transcription	Brain Substantia Nigra	brain
25	chr6:114661400-114665200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr6:114661400-114665400	Active TSS	H9 Cell Line	embryonic stem cell
27	chr6:114661400-114665600	Active TSS	Brain Angular Gyrus	brain
28	chr6:114661600-114661800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr6:114661600-114662200	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:114661600-114662400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:114661600-114665000	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr6:114661600-114665200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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