Variant report

Variant	rs6939101
Chromosome Location	chr6:142410321-142410322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr6:142409718-142410575	A549	lung:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
2	MAX	chr6:142410054-142410331	H1-hESC	embryonic stem cell:	n/a	n/a
3	REST	chr6:142409953-142410457	A549	lung:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
4	TEAD4	chr6:142409864-142410537	A549	lung:	n/a	n/a
5	REST	chr6:142410058-142410325	PFSK-1	brain:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
6	SIN3AK20	chr6:142409810-142410543	MCF-7	breast:	n/a	n/a
7	RAD21	chr6:142409973-142410396	H1-hESC	embryonic stem cell:	n/a	chr6:142410215-142410228
8	TEAD4	chr6:142409991-142410344	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAFK	chr6:142410108-142410427	H1-hESC	embryonic stem cell:	n/a	n/a
10	REST	chr6:142409924-142410463	PFSK-1	brain:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
11	REST	chr6:142410052-142410335	HepG2	liver:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
12	GTF2F1	chr6:142410147-142410328	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr6:142409961-142410409	H1-hESC	embryonic stem cell:	n/a	n/a
14	REST	chr6:142409784-142410443	SK-N-SH	brain:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
15	REST	chr6:142410021-142410402	U87	brain:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
16	REST	chr6:142409635-142410611	MCF-7	breast:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
17	REST	chr6:142409654-142410759	HL-60	blood:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
18	RCOR1	chr6:142409815-142410450	IMR90	lung:	n/a	n/a
19	REST	chr6:142410061-142410440	HCT-116	colon:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
20	HDAC2	chr6:142409918-142410421	MCF-7	breast:	n/a	n/a
21	MAFF	chr6:142410285-142410432	HepG2	liver:	n/a	n/a
22	REST	chr6:142410021-142410343	U87	brain:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
23	REST	chr6:142410067-142410341	GM12878	blood:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
24	MXI1	chr6:142410046-142410334	H1-hESC	embryonic stem cell:	n/a	n/a
25	ELF1	chr6:142410020-142410454	MCF-7	breast:	n/a	n/a
26	SP1	chr6:142410044-142410424	H1-hESC	embryonic stem cell:	n/a	n/a
27	RCOR1	chr6:142410039-142410326	K562	blood:	n/a	n/a
28	REST	chr6:142409698-142410745	MCF-7	breast:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
29	REST	chr6:142409857-142410504	PFSK-1	brain:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
30	MAX	chr6:142410051-142410414	H1-hESC	embryonic stem cell:	n/a	n/a
31	REST	chr6:142409898-142410530	HL-60	blood:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
32	TAF7	chr6:142410013-142410410	H1-hESC	embryonic stem cell:	n/a	n/a
33	GATA3	chr6:142410017-142410446	MCF-7	breast:	n/a	n/a
34	REST	chr6:142409922-142410454	K562	blood:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
35	RCOR1	chr6:142410099-142410323	HepG2	liver:	n/a	n/a
36	SIN3AK20	chr6:142409949-142410406	MCF-7	breast:	n/a	n/a
37	REST	chr6:142410043-142410394	HCT-116	colon:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
38	YY1	chr6:142409967-142410341	H1-hESC	embryonic stem cell:	n/a	chr6:142410244-142410258
39	SPI1	chr6:142409922-142410414	HL-60	blood:	n/a	n/a
40	SIN3AK20	chr6:142409999-142410358	SK-N-SH	brain:	n/a	n/a
41	REST	chr6:142409722-142410484	H1-hESC	embryonic stem cell:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
42	MAX	chr6:142409938-142410436	MCF-7	breast:	n/a	n/a
43	REST	chr6:142410002-142410418	HepG2	liver:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
44	REST	chr6:142409808-142410510	HepG2	liver:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
45	JUND	chr6:142410051-142410372	H1-hESC	embryonic stem cell:	n/a	n/a
46	ATF2	chr6:142409951-142410378	H1-hESC	embryonic stem cell:	n/a	n/a
47	ZNF143	chr6:142410018-142410390	H1-hESC	embryonic stem cell:	n/a	n/a
48	REST	chr6:142409666-142410760	ECC-1	luminal epithelium:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
49	REST	chr6:142410057-142410328	SK-N-SH	brain:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
50	REST	chr6:142409600-142410509	H1-hESC	embryonic stem cell:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213

Variant related genes	Relation type
NMBR	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17071519	1.00[AMR][1000 genomes]
rs58709297	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58919399	1.00[AMR][1000 genomes]
rs6909493	1.00[AMR][1000 genomes]
rs6915499	1.00[AMR][1000 genomes]
rs6937855	1.00[AMR][1000 genomes]
rs7762535	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	nsv886732	chr6:142290338-142536049	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv886733	chr6:142316672-142514226	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	20 gene(s)	inside rSNPs	diseases
3	nsv1027489	chr6:142336722-142429903	Bivalent Enhancer Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv886734	chr6:142347611-142523865	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv830824	chr6:142361107-142544929	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv886735	chr6:142365171-142472294	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv886736	chr6:142365171-142523865	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142409200-142410400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
2	chr6:142409400-142410400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:142409400-142410400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
4	chr6:142409600-142410400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:142409600-142410400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
6	chr6:142409600-142410400	Bivalent Enhancer	Ovary	ovary
7	chr6:142409800-142410400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:142409800-142410400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:142409800-142410400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
10	chr6:142409800-142410400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr6:142410000-142410400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:142410000-142410400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr6:142410000-142410400	Enhancers	Placenta	Placenta
14	chr6:142410200-142410400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:142410200-142410400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
16	chr6:142410200-142410400	Bivalent Enhancer	Primary T cells from cord blood	blood
17	chr6:142410200-142410400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
18	chr6:142410200-142410400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:142410200-142410400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr6:142410200-142410400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
21	chr6:142410200-142410400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:142410200-142410400	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
23	chr6:142410200-142410400	Enhancers	Right Ventricle	heart
24	chr6:142410200-142410600	Active TSS	Fetal Brain Female	brain

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