Variant report

Variant	rs200858
Chromosome Location	chr6:5085388-5085389
allele	C/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	POLR2A	chr6:5084657-5085423	Hela-S3	cervix:	n/a	n/a
2	ZNF263	chr6:5084656-5086573	HEK293-T-REx	kidney:	n/a	chr6:5085514-5085523
3	POLR2A	chr6:5084435-5085862	GM12892	blood:	n/a	n/a
4	MAX	chr6:5084978-5085516	ECC-1	luminal epithelium:	n/a	chr6:5085239-5085248 chr6:5085238-5085245
5	MTA3	chr6:5085003-5085466	GM12878	blood:	n/a	n/a
6	MAZ	chr6:5084505-5085543	Hela-S3	cervix:	n/a	chr6:5085239-5085248 chr6:5084689-5084698 chr6:5085238-5085245
7	MXI1	chr6:5085095-5085395	GM12878	blood:	n/a	n/a
8	MAZ	chr6:5084458-5086460	IMR90	lung:	n/a	chr6:5085239-5085248 chr6:5084689-5084698 chr6:5085238-5085245
9	CTBP2	chr6:5084541-5085419	H1-hESC	embryonic stem cell:	n/a	n/a
10	SMARCB1	chr6:5084261-5086221	Hela-S3	cervix:	n/a	n/a
11	MAX	chr6:5084574-5086339	A549	lung:	n/a	chr6:5085239-5085248 chr6:5084689-5084698 chr6:5085238-5085245
12	BHLHE40	chr6:5084524-5085406	GM12878	blood:	n/a	chr6:5084890-5084906 chr6:5084923-5084939 chr6:5084823-5084839
13	POLR2A	chr6:5084720-5085419	GM12878	blood:	n/a	n/a
14	BACH1	chr6:5085023-5085434	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr6:5084561-5086335	GM12878	blood:	n/a	n/a
16	CTCF	chr6:5085280-5085430	GM12875	blood:	n/a	n/a
17	CTCF	chr6:5085320-5085470	WERI-Rb-1	eye:	n/a	n/a
18	CTCF	chr6:5085340-5085490	NHLF	lung:	n/a	n/a
19	CTCF	chr6:5085240-5085390	GM12864	blood:	n/a	n/a
20	POLR2A	chr6:5082575-5085730	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr6:5085320-5085470	AG09319	gingival:	n/a	n/a
22	MAX	chr6:5084448-5086348	A549	lung:	n/a	chr6:5085239-5085248 chr6:5084689-5084698 chr6:5085238-5085245
23	POLR2A	chr6:5084497-5085982	GM18505	blood:	n/a	n/a
24	SIN3A	chr6:5085052-5085679	H1-hESC	embryonic stem cell:	n/a	chr6:5085529-5085542
25	MAX	chr6:5085061-5085532	GM12878	blood:	n/a	chr6:5085239-5085248 chr6:5085238-5085245
26	POLR2A	chr6:5084386-5085402	K562	blood:	n/a	n/a
27	HMGN3	chr6:5084446-5085450	K562	blood:	n/a	n/a
28	E2F6	chr6:5084844-5087368	H1-hESC	embryonic stem cell:	n/a	chr6:5085074-5085089 chr6:5085073-5085082 chr6:5084902-5084911 chr6:5084924-5084934
29	SUZ12	chr6:5084919-5085727	H1-hESC	embryonic stem cell:	n/a	n/a
30	ZBTB7A	chr6:5084420-5085593	ECC-1	luminal epithelium:	n/a	chr6:5084709-5084717
31	MAZ	chr6:5084434-5086056	GM12878	blood:	n/a	chr6:5085239-5085248 chr6:5084689-5084698 chr6:5085238-5085245
32	ZBTB7A	chr6:5084358-5085535	ECC-1	luminal epithelium:	n/a	chr6:5084709-5084717
33	POLR2A	chr6:5084507-5086239	GM12892	blood:	n/a	n/a
34	CTCF	chr6:5085240-5085390	WERI-Rb-1	eye:	n/a	n/a
35	RCOR1	chr6:5084999-5085770	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5082094..5085573-chr6:5086074..5088451,3	K562	blood:

Variant related genes	Relation type
PPP1R3G	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs400390	0.81[EUR][1000 genomes]
rs437695	0.84[EUR][1000 genomes]
rs439350	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs451476	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs666518	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1017373	chr6:5066785-5128943	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv538112	chr6:5066785-5128943	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
10	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	esv3439309	chr6:5084978-5087526	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5080400-5085400	Flanking Active TSS	HepG2	liver
2	chr6:5084200-5086000	Active TSS	Right Ventricle	heart
3	chr6:5084200-5087400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:5084400-5085400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:5084400-5085400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:5084400-5085400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:5084400-5085400	Bivalent/Poised TSS	Colonic Mucosa	Colon
8	chr6:5084400-5085400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
9	chr6:5084400-5085600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr6:5084400-5085600	Bivalent/Poised TSS	Spleen	Spleen
11	chr6:5084400-5085800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:5084400-5085800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:5084400-5085800	Active TSS	Fetal Kidney	kidney
14	chr6:5084400-5086000	Active TSS	Liver	Liver
15	chr6:5084400-5086000	Bivalent/Poised TSS	Fetal Brain Female	brain
16	chr6:5084400-5086200	Active TSS	A549	lung
17	chr6:5084400-5086400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
18	chr6:5084400-5086400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:5084400-5086400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr6:5084400-5086400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr6:5084400-5086400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:5084400-5086400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr6:5084400-5086400	Active TSS	Brain Angular Gyrus	brain
24	chr6:5084400-5086400	Active TSS	Brain Cingulate Gyrus	brain
25	chr6:5084400-5086400	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr6:5084400-5086400	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr6:5084400-5086400	Active TSS	Left Ventricle	heart
28	chr6:5084400-5086400	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr6:5084400-5086400	Active TSS	Right Atrium	heart
30	chr6:5084400-5086600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
31	chr6:5084400-5086600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
32	chr6:5084400-5086600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:5084400-5086600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
34	chr6:5084400-5086600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:5084400-5086600	Active TSS	Colon Smooth Muscle	Colon
36	chr6:5084400-5086600	Active TSS	Ovary	ovary
37	chr6:5084400-5086800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
38	chr6:5084400-5086800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
39	chr6:5084400-5086800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
40	chr6:5084400-5086800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:5084400-5086800	Active TSS	Brain Anterior Caudate	brain
42	chr6:5084400-5086800	Active TSS	Brain Substantia Nigra	brain
43	chr6:5084400-5086800	Active TSS	Psoas Muscle	Psoas
44	chr6:5084400-5087000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:5084400-5087000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
46	chr6:5084400-5087000	Bivalent Enhancer	Fetal Brain Male	brain
47	chr6:5084400-5087000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
48	chr6:5084400-5087200	Active TSS	Rectal Smooth Muscle	rectum
49	chr6:5084600-5085400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr6:5084600-5085600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell

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