Variant report

Variant	rs11958544
Chromosome Location	chr5:115151326-115151327
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	chr5:115151061-115153120	H1-neurons	neurons:	n/a	chr5:115152626-115152639
2	RAD21	chr5:115151181-115152241	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr5:115151220-115151370	AG04449	skin:	n/a	n/a
4	CTCF	chr5:115151220-115151370	GM12866	blood:	n/a	n/a
5	JUND	chr5:115151296-115152876	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr5:115151132-115152960	H1-neurons	neurons:	n/a	n/a
7	CTCF	chr5:115151240-115151390	HPF	lung:	n/a	n/a
8	ZNF263	chr5:115150963-115152852	HEK293-T-REx	kidney:	n/a	n/a
9	CTCF	chr5:115151200-115151350	SK-N-SH_RA	brain:	n/a	n/a
10	POLR2A	chr5:115151190-115152887	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr5:115151205-115152841	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr5:115151260-115151410	AoAF	blood vessel:	n/a	n/a
13	CTCF	chr5:115151180-115151330	HPAF	blood vessel:	n/a	n/a
14	CTCF	chr5:115151300-115151450	SK-N-SH_RA	brain:	n/a	n/a
15	CTCF	chr5:115151220-115151370	HUVEC	blood vessel:	n/a	n/a
16	MAX	chr5:115151322-115152818	H1-hESC	embryonic stem cell:	n/a	chr5:115151855-115151864
17	SIN3A	chr5:115151138-115152731	H1-hESC	embryonic stem cell:	n/a	chr5:115151909-115151920

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115149403..115152060-chr5:115175796..115178394,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP3S1-1	chr5:115150892-115151615	ENSG00000248017

Variant related genes	Relation type
CDO1	TF binding region
ENSG00000145782	Chromatin interaction
ENSG00000177879	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10058994	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs10059199	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10070325	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10074061	0.89[AFR][1000 genomes]
rs10519429	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs11951965	0.83[AMR][1000 genomes]
rs11959669	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12782	0.83[AMR][1000 genomes]
rs1968365	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs4920893	0.90[AFR][1000 genomes]
rs4920894	0.83[AMR][1000 genomes]
rs60326315	0.83[AMR][1000 genomes]
rs6872587	0.90[AFR][1000 genomes]
rs73259615	0.83[AMR][1000 genomes]
rs73265491	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs73265501	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9326975	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115149000-115151800	Active TSS	Right Atrium	heart
2	chr5:115149200-115152800	Active TSS	Aorta	Aorta
3	chr5:115149600-115151600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:115149600-115152200	Bivalent/Poised TSS	Psoas Muscle	Psoas
5	chr5:115149800-115151400	Active TSS	Placenta	Placenta
6	chr5:115149800-115153000	Active TSS	Liver	Liver
7	chr5:115150200-115152600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:115150600-115151400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
9	chr5:115150600-115151600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:115150600-115152000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:115150600-115153000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr5:115150800-115151400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
13	chr5:115150800-115151400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
14	chr5:115150800-115151400	Flanking Active TSS	Brain Hippocampus Middle	brain
15	chr5:115150800-115151400	Flanking Bivalent TSS/Enh	NH-A	brain
16	chr5:115150800-115151600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:115150800-115151800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:115150800-115152000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
19	chr5:115150800-115152400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
20	chr5:115150800-115152600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
21	chr5:115150800-115152800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:115150800-115152800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr5:115150800-115152800	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr5:115150800-115153400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr5:115151000-115151400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
26	chr5:115151000-115151400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:115151000-115151400	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
28	chr5:115151000-115151400	Flanking Active TSS	Brain Substantia Nigra	brain
29	chr5:115151000-115151400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr5:115151000-115151400	Bivalent/Poised TSS	Left Ventricle	heart
31	chr5:115151000-115151400	Flanking Active TSS	Ovary	ovary
32	chr5:115151000-115151400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
33	chr5:115151000-115151600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr5:115151000-115151600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
35	chr5:115151000-115151600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
36	chr5:115151000-115151600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr5:115151000-115151600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
38	chr5:115151000-115151600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
39	chr5:115151000-115151600	Active TSS	Right Ventricle	heart
40	chr5:115151000-115151800	Bivalent Enhancer	Fetal Thymus	thymus
41	chr5:115151000-115152200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
42	chr5:115151000-115152200	Flanking Bivalent TSS/Enh	Osteobl	bone
43	chr5:115151000-115152400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
44	chr5:115151000-115152600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:115151000-115152800	Active TSS	H9 Cell Line	embryonic stem cell
46	chr5:115151000-115152800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
47	chr5:115151000-115152800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr5:115151000-115152800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
49	chr5:115151000-115152800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
50	chr5:115151000-115153000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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