Variant report

Variant	rs1563911
Chromosome Location	chr5:7850055-7850056
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	SIN3A	chr5:7849859-7850600	H1-hESC	embryonic stem cell:	n/a	chr5:7850037-7850048
2	RAD21	chr5:7849688-7850320	H1-hESC	embryonic stem cell:	n/a	chr5:7849926-7849938 chr5:7850138-7850157 chr5:7850147-7850156 chr5:7850001-7850015
3	CTCF	chr5:7850020-7850170	HCM	heart:	n/a	chr5:7850135-7850156 chr5:7850147-7850154 chr5:7850140-7850158
4	E2F6	chr5:7849741-7850257	H1-hESC	embryonic stem cell:	n/a	chr5:7849940-7849952 chr5:7849941-7849948 chr5:7849941-7849948 chr5:7849941-7849948 chr5:7850062-7850074
5	CTCF	chr5:7850026-7850294	GM12878	blood:	n/a	chr5:7850135-7850156 chr5:7850147-7850154 chr5:7850140-7850158
6	CTCF	chr5:7849869-7850345	SK-N-SH	brain:	n/a	chr5:7850135-7850156 chr5:7849883-7849896 chr5:7850147-7850154 chr5:7850140-7850158
7	ZNF143	chr5:7850020-7850511	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr5:7849708-7850344	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr5:7849940-7850090	HVMF	connective:	n/a	n/a
10	CTCF	chr5:7849980-7850130	MCF-7	breast:	n/a	n/a
11	JUND	chr5:7850033-7850230	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr5:7849960-7850110	HRE	kidney:	n/a	n/a
13	CTCF	chr5:7850040-7850190	HMEC	breast:	n/a	chr5:7850135-7850156 chr5:7850147-7850154 chr5:7850140-7850158
14	RAD21	chr5:7849670-7850378	H1-hESC	embryonic stem cell:	n/a	chr5:7849926-7849938 chr5:7850138-7850157 chr5:7850147-7850156 chr5:7850001-7850015
15	RAD21	chr5:7850045-7850229	SK-N-SH_RA	brain:	n/a	chr5:7850138-7850157 chr5:7850147-7850156
16	E2F6	chr5:7849518-7850395	H1-hESC	embryonic stem cell:	n/a	chr5:7849940-7849952 chr5:7850372-7850381 chr5:7849941-7849948 chr5:7849941-7849948 chr5:7849941-7849948 chr5:7850062-7850074
17	TBP	chr5:7850013-7850253	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr5:7850000-7850150	NHLF	lung:	n/a	n/a
19	CTCF	chr5:7850020-7850170	Caco-2	colon:	n/a	chr5:7850135-7850156 chr5:7850147-7850154 chr5:7850140-7850158
20	CTCF	chr5:7850000-7850150	GM06990	blood:	n/a	n/a
21	CTCF	chr5:7850047-7850204	SK-N-SH_RA	brain:	n/a	chr5:7850135-7850156 chr5:7850147-7850154 chr5:7850140-7850158
22	CTCF	chr5:7850020-7850170	AG04450	lung:	n/a	chr5:7850135-7850156 chr5:7850147-7850154 chr5:7850140-7850158
23	SIN3AK20	chr5:7849989-7850474	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr5:7850040-7850190	RPTEC	kidney:	n/a	chr5:7850135-7850156 chr5:7850147-7850154 chr5:7850140-7850158
25	CTCF	chr5:7850004-7850249	HepG2	liver:	n/a	chr5:7850135-7850156 chr5:7850147-7850154 chr5:7850140-7850158
26	ZBTB7A	chr5:7850031-7850189	HepG2	liver:	n/a	n/a
27	CTCF	chr5:7850040-7850190	NHEK	skin:	n/a	chr5:7850135-7850156 chr5:7850147-7850154 chr5:7850140-7850158
28	RAD21	chr5:7849938-7850319	H1-hESC	embryonic stem cell:	n/a	chr5:7850138-7850157 chr5:7850147-7850156 chr5:7850001-7850015
29	CTCF	chr5:7849970-7850307	H1-hESC	embryonic stem cell:	n/a	chr5:7850135-7850156 chr5:7850147-7850154 chr5:7850140-7850158
30	MAX	chr5:7849735-7850194	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:7849253..7853514-chr5:7868734..7871211,5	MCF-7	breast:
2	chr5:7843515..7845259-chr5:7848179..7851160,2	MCF-7	breast:

Variant related genes	Relation type
MTRR	TF binding region
ENSG00000124279	Chromatin interaction
ENSG00000124275	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1005101	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1108209	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12653983	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1993716	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1993717	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57110438	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57580763	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73737638	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7714950	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[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	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS 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	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv461927	chr5:7757812-7854289	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv597004	chr5:7757812-7854289	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3436798	chr5:7849477-7852325	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv3440712	chr5:7849552-7852150	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7849000-7850200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr5:7849000-7851000	Weak transcription	HSMM	muscle
3	chr5:7849400-7850400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:7849600-7850200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr5:7849600-7850200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:7849600-7850200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
7	chr5:7849600-7850200	Flanking Active TSS	Brain Germinal Matrix	brain
8	chr5:7849600-7850200	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr5:7849600-7850200	Enhancers	Fetal Heart	heart
10	chr5:7849600-7850400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:7849600-7850400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
12	chr5:7849600-7850400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
13	chr5:7849600-7850400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
14	chr5:7849600-7851400	Active TSS	Brain Angular Gyrus	brain
15	chr5:7849600-7851800	Active TSS	H9 Cell Line	embryonic stem cell
16	chr5:7849600-7851800	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr5:7849800-7850200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:7849800-7850200	Bivalent/Poised TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:7849800-7850200	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:7849800-7850200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
21	chr5:7849800-7850200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
22	chr5:7849800-7850200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr5:7849800-7850200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:7849800-7850200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
25	chr5:7849800-7850200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
26	chr5:7849800-7850200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
27	chr5:7849800-7850200	Flanking Bivalent TSS/Enh	Thymus	Thymus
28	chr5:7849800-7850400	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:7849800-7850400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
30	chr5:7849800-7850400	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:7849800-7850400	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
32	chr5:7849800-7850400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:7849800-7850400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
34	chr5:7849800-7850400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
35	chr5:7849800-7850400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
36	chr5:7849800-7850400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
37	chr5:7849800-7850400	Enhancers	Fetal Brain Male	brain
38	chr5:7849800-7850400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
39	chr5:7849800-7850400	Enhancers	Gastric	stomach
40	chr5:7849800-7850400	Flanking Active TSS	Right Ventricle	heart
41	chr5:7849800-7850400	Bivalent Enhancer	HMEC	breast
42	chr5:7849800-7850400	Bivalent Enhancer	HUVEC	blood vessel
43	chr5:7849800-7850600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
44	chr5:7849800-7850600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
45	chr5:7849800-7850600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
46	chr5:7849800-7850600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr5:7849800-7850600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:7849800-7850600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr5:7849800-7850600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
50	chr5:7849800-7850600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle

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