Variant report

Variant	rs3811088
Chromosome Location	chr6:142410112-142410113
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	TAF7	chr6:142410065-142410295	H1-hESC	embryonic stem cell:	n/a	n/a
4	REST	chr6:142409953-142410457	A549	lung:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
5	TEAD4	chr6:142409864-142410537	A549	lung:	n/a	n/a
6	REST	chr6:142410058-142410325	PFSK-1	brain:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
7	SIN3AK20	chr6:142409810-142410543	MCF-7	breast:	n/a	n/a
8	RAD21	chr6:142409973-142410396	H1-hESC	embryonic stem cell:	n/a	chr6:142410215-142410228
9	EBF1	chr6:142410042-142410233	GM12878	blood:	n/a	chr6:142410141-142410152 chr6:142410141-142410151 chr6:142410142-142410151 chr6:142410140-142410153
10	TEAD4	chr6:142409991-142410344	H1-hESC	embryonic stem cell:	n/a	n/a
11	EBF1	chr6:142409999-142410306	GM12878	blood:	n/a	chr6:142410141-142410152 chr6:142410141-142410151 chr6:142410142-142410151 chr6:142410140-142410153
12	MAFK	chr6:142410108-142410427	H1-hESC	embryonic stem cell:	n/a	n/a
13	REST	chr6:142409924-142410463	PFSK-1	brain:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
14	REST	chr6:142410052-142410335	HepG2	liver:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
15	SIN3AK20	chr6:142410007-142410268	K562	blood:	n/a	n/a
16	ZNF143	chr6:142410089-142410202	GM12878	blood:	n/a	n/a
17	MAX	chr6:142409961-142410409	H1-hESC	embryonic stem cell:	n/a	n/a
18	ZNF384	chr6:142410044-142410152	K562	blood:	n/a	n/a
19	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
20	MAX	chr6:142409936-142410304	ECC-1	luminal epithelium:	n/a	n/a
21	BACH1	chr6:142409948-142410277	H1-hESC	embryonic stem cell:	n/a	n/a
22	REST	chr6:142410021-142410402	U87	brain:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
23	REST	chr6:142409635-142410611	MCF-7	breast:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
24	REST	chr6:142409654-142410759	HL-60	blood:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
25	RCOR1	chr6:142409815-142410450	IMR90	lung:	n/a	n/a
26	REST	chr6:142410061-142410440	HCT-116	colon:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
27	HDAC2	chr6:142409918-142410421	MCF-7	breast:	n/a	n/a
28	REST	chr6:142410021-142410343	U87	brain:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
29	REST	chr6:142410067-142410341	GM12878	blood:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
30	EBF1	chr6:142409987-142410258	GM12878	blood:	n/a	chr6:142410141-142410152 chr6:142410141-142410151 chr6:142410142-142410151 chr6:142410140-142410153
31	MXI1	chr6:142410046-142410334	H1-hESC	embryonic stem cell:	n/a	n/a
32	ELF1	chr6:142410020-142410454	MCF-7	breast:	n/a	n/a
33	SP1	chr6:142410044-142410424	H1-hESC	embryonic stem cell:	n/a	n/a
34	RCOR1	chr6:142410039-142410326	K562	blood:	n/a	n/a
35	REST	chr6:142409698-142410745	MCF-7	breast:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
36	REST	chr6:142409857-142410504	PFSK-1	brain:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
37	MAX	chr6:142410051-142410414	H1-hESC	embryonic stem cell:	n/a	n/a
38	ZNF217	chr6:142410028-142410289	MCF-7	breast:	n/a	n/a
39	REST	chr6:142409898-142410530	HL-60	blood:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
40	TCF12	chr6:142410102-142410308	H1-hESC	embryonic stem cell:	n/a	n/a
41	TAF7	chr6:142410013-142410410	H1-hESC	embryonic stem cell:	n/a	n/a
42	GATA3	chr6:142410017-142410446	MCF-7	breast:	n/a	n/a
43	REST	chr6:142409922-142410454	K562	blood:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
44	RCOR1	chr6:142410099-142410323	HepG2	liver:	n/a	n/a
45	SIN3AK20	chr6:142409949-142410406	MCF-7	breast:	n/a	n/a
46	REST	chr6:142410043-142410394	HCT-116	colon:	n/a	chr6:142410204-142410224 chr6:142410135-142410144 chr6:142410207-142410220 chr6:142410133-142410141 chr6:142410204-142410213
47	GATA3	chr6:142409949-142410276	T-47D	breast:	n/a	n/a
48	YY1	chr6:142409967-142410341	H1-hESC	embryonic stem cell:	n/a	chr6:142410244-142410258
49	SPI1	chr6:142409922-142410414	HL-60	blood:	n/a	n/a
50	SIN3AK20	chr6:142409999-142410358	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:142410098-142410148	GM06990	blood:	n/a
2	chr6:142410100-142410150	HAEpiC	amniotic membrane:	n/a
3	chr6:142410098-142410148	HRCEpiC	kidney:	n/a
4	chr6:142410098-142410148	GM12892	blood:	n/a
5	chr6:142410100-142410150	SK-N-MC	brain:	n/a
6	chr6:142410100-142410150	AG04450	lung:	fetal
7	chr6:142410098-142410148	HCF	heart:	n/a
8	chr6:142410100-142410150	PFSK-1	brain:	n/a
9	chr6:142410100-142410150	BJ	skin:	n/a
10	chr6:142410098-142410148	HRPEpiC	eye:	n/a
11	chr6:142410098-142410148	NT2-D1	testis:	n/a
12	chr6:142410098-142410148	ProgFib	skin:	n/a
13	chr6:142410100-142410150	Caco-2	colon:	n/a
14	chr6:142410100-142410150	LNCaP	prostate:	n/a
15	chr6:142410098-142410148	SKMC	muscle:	n/a
16	chr6:142410100-142410150	K562	blood:	n/a
17	chr6:142410098-142410148	HEEpiC	esophagus:	n/a
18	chr6:142410098-142410148	PrEC	prostate:	n/a
19	chr6:142410098-142410148	HMEC	breast:	n/a
20	chr6:142410098-142410148	AoSMC	blood vessel:	n/a
21	chr6:142410100-142410150	ECC-1	luminal epithelium:	n/a
22	chr6:142410100-142410150	GM12891	blood:	n/a
23	chr6:142410100-142410150	BE2_C	brain:	n/a
24	chr6:142410098-142410148	HEK293	kidney:	embryo
25	chr6:142410100-142410150	AoSMC	blood vessel:	n/a
26	chr6:142410100-142410150	AG09309	skin:	n/a
27	chr6:142410100-142410150	NT2-D1	testis:	n/a
28	chr6:142410098-142410148	K562	blood:	n/a
29	chr6:142410100-142410150	ProgFib	skin:	n/a
30	chr6:142410098-142410148	MCF10A-Er-Src	breast:	n/a
31	chr6:142410098-142410148	AG04450	lung:	fetal
32	chr6:142410098-142410148	SK-N-MC	brain:	n/a
33	chr6:142410100-142410150	NHDF-neo	bronchial:	n/a
34	chr6:142410100-142410150	AG09319	gingival:	n/a
35	chr6:142410098-142410148	Caco-2	colon:	n/a
36	chr6:142410100-142410150	HRCEpiC	kidney:	n/a
37	chr6:142410098-142410148	SAEC	small airway:	n/a
38	chr6:142410100-142410150	SKMC	muscle:	n/a
39	chr6:142410100-142410150	MCF10A-Er-Src	breast:	n/a
40	chr6:142410100-142410150	T-47D	breast:	n/a
41	chr6:142410098-142410148	HL-60	blood:	n/a
42	chr6:142410098-142410148	PANC-1	pancreas:	n/a
43	chr6:142410100-142410150	CMK	blood:	n/a
44	chr6:142410100-142410150	GM12878	blood:	n/a
45	chr6:142410100-142410150	U87	brain:	n/a
46	chr6:142410100-142410150	ovcar-3	ovarian:	n/a
47	chr6:142410098-142410148	A549	lung:	n/a
48	chr6:142410098-142410148	HUVEC	blood vessel:	n/a
49	chr6:142410098-142410148	NH-A	brain:	n/a
50	chr6:142410100-142410150	IMR90	lung:	fetal

Variant related genes	Relation type
NMBR	TF binding region
NMBR	CpG island

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs225648	0.93[GIH][hapmap];0.89[JPT][hapmap]
rs225699	0.91[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap]
rs3811083	0.84[JPT][hapmap]
rs4896569	0.80[ASN][1000 genomes]
rs4896576	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6902780	0.81[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs6926279	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs6934439	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6940882	0.84[JPT][hapmap]
rs7740687	0.80[ASN][1000 genomes]
rs7742164	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7756224	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7758432	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7766528	0.80[ASN][1000 genomes]
rs9373333	0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs9373334	0.80[ASN][1000 genomes]
rs9385985	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs9484589	0.80[ASN][1000 genomes]
rs9484591	0.80[ASN][1000 genomes]
rs9484600	0.84[JPT][hapmap]
rs9496241	0.80[ASN][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:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142409200-142410200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
2	chr6:142409200-142410200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr6:142409200-142410200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:142409200-142410200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:142409200-142410200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:142409200-142410200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr6:142409200-142410200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr6:142409200-142410200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:142409200-142410400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr6:142409400-142410200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr6:142409400-142410200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
12	chr6:142409400-142410400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:142409400-142410400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
14	chr6:142409600-142410200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:142409600-142410200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
16	chr6:142409600-142410200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
17	chr6:142409600-142410200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
18	chr6:142409600-142410400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:142409600-142410400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
20	chr6:142409600-142410400	Bivalent Enhancer	Ovary	ovary
21	chr6:142409800-142410200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr6:142409800-142410200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:142409800-142410200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
24	chr6:142409800-142410200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:142409800-142410200	Bivalent/Poised TSS	Fetal Brain Male	brain
26	chr6:142409800-142410200	Bivalent/Poised TSS	Fetal Brain Female	brain
27	chr6:142409800-142410200	Flanking Active TSS	NH-A	brain
28	chr6:142409800-142410400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:142409800-142410400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:142409800-142410400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
31	chr6:142409800-142410400	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr6:142410000-142410200	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:142410000-142410200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:142410000-142410200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:142410000-142410200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
36	chr6:142410000-142410200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
37	chr6:142410000-142410200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:142410000-142410200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:142410000-142410200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:142410000-142410200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
41	chr6:142410000-142410200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr6:142410000-142410400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr6:142410000-142410400	Enhancers	Muscle Satellite Cultured Cells	--
44	chr6:142410000-142410400	Enhancers	Placenta	Placenta

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