Variant report

Variant	rs11949902
Chromosome Location	chr5:1931060-1931061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr5:1930809-1931676	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr5:1927991-1933825	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr5:1928300-1932687	MCF10A-Er-Src	breast:	n/a	n/a
4	TBP	chr5:1931044-1931838	H1-hESC	embryonic stem cell:	n/a	n/a
5	MYC	chr5:1930845-1931365	MCF10A-Er-Src	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:1931058-1931108	HEK293	kidney:	embryo
2	chr5:1931058-1931108	SK-N-SH_RA	brain:	n/a
3	chr5:1931058-1931108	HCPEpiC	choroid plexus:	n/a
4	chr5:1931058-1931108	AG04449	skin:	fetal
5	chr5:1931058-1931108	PANC-1	pancreas:	n/a
6	chr5:1931058-1931108	AG10803	skin:	n/a
7	chr5:1931058-1931108	K562	blood:	n/a
8	chr5:1931058-1931108	T-47D	breast:	n/a
9	chr5:1931058-1931108	SK-N-SH	brain:	n/a
10	chr5:1931058-1931108	CMK	blood:	n/a
11	chr5:1931058-1931108	GM12891	blood:	n/a
12	chr5:1931058-1931108	HIPEpiC	eye:	n/a
13	chr5:1931058-1931108	AG09319	gingival:	n/a
14	chr5:1931058-1931108	HPAEpiC	pulmonary alveolar:	n/a
15	chr5:1931058-1931108	Hepatocyte	liver:	n/a
16	chr5:1931058-1931108	MCF-7	breast:	n/a
17	chr5:1931058-1931108	SK-N-MC	brain:	n/a
18	chr5:1931058-1931108	AG09309	skin:	n/a
19	chr5:1931058-1931108	HepG2	liver:	n/a
20	chr5:1931058-1931108	NT2-D1	testis:	n/a
21	chr5:1931058-1931108	PrEC	prostate:	n/a
22	chr5:1931058-1931108	PFSK-1	brain:	n/a
23	chr5:1931058-1931108	RPTEC	kidney:	n/a
24	chr5:1931058-1931108	SKMC	muscle:	n/a
25	chr5:1931058-1931108	BJ	skin:	n/a
26	chr5:1931058-1931108	AG04450	lung:	fetal
27	chr5:1931058-1931108	HAEpiC	amniotic membrane:	n/a
28	chr5:1931058-1931108	HNPCEpiC	eye:	n/a
29	chr5:1931058-1931108	HRPEpiC	eye:	n/a
30	chr5:1931058-1931108	HUVEC	blood vessel:	n/a
31	chr5:1931058-1931108	AoSMC	blood vessel:	n/a
32	chr5:1931058-1931108	ECC-1	luminal epithelium:	n/a
33	chr5:1931058-1931108	H1-hESC	embryonic stem cell:	embryo
34	chr5:1931058-1931108	NHBE	bronchial:	n/a
35	chr5:1931058-1931108	NH-A	brain:	n/a
36	chr5:1931058-1931108	HL-60	blood:	n/a
37	chr5:1931058-1931108	HMEC	breast:	n/a
38	chr5:1931058-1931108	Jurkat	blood:	n/a
39	chr5:1931058-1931108	LNCaP	prostate:	n/a
40	chr5:1931058-1931108	HCT-116	colon:	n/a
41	chr5:1931058-1931108	HCM	heart:	n/a
42	chr5:1931058-1931108	BE2_C	brain:	n/a
43	chr5:1931058-1931108	GM12878	blood:	n/a
44	chr5:1931058-1931108	GM19239	blood:	n/a
45	chr5:1931058-1931108	Hela-S3	cervix:	n/a
46	chr5:1931058-1931108	U87	brain:	n/a
47	chr5:1931058-1931108	HCF	heart:	n/a
48	chr5:1931058-1931108	HRCEpiC	kidney:	n/a
49	chr5:1931058-1931108	HRE	kidney:	n/a
50	chr5:1931058-1931108	HEEpiC	esophagus:	n/a

No data

Variant related genes	Relation type
ENSG00000248994	TF binding region
ENSG00000248994	CpG island

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10072848	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10462748	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11952878	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11959614	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13162440	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16901995	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4478361	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975765	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4975766	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62337068	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6420032	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6420033	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6555020	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6555022	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6555023	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6555024	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6555025	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6555026	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6555027	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6555029	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6861662	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6862005	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6865822	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6881134	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6890530	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6897356	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7444179	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7444647	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7713748	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
3	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv881557	chr5:1822326-1932463	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv880886	chr5:1880891-1936443	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv880460	chr5:1886471-1936443	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv881650	chr5:1892995-1944487	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv880653	chr5:1892995-1946697	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv1015576	chr5:1894124-1942909	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv880562	chr5:1895829-1936443	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv881174	chr5:1895829-1942834	Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv880381	chr5:1895829-1946697	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv508344	chr5:1905222-1976860	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv881562	chr5:1907974-1976187	Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv880964	chr5:1912921-1953161	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
18	nsv596897	chr5:1924628-1934490	Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
19	esv3429117	chr5:1927452-1931450	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	esv3379236	chr5:1927852-1931550	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	esv3382920	chr5:1927852-1931550	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11949902	RP11-259O2.1	cis	Artery Tibial	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1929600-1931400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:1929800-1931200	Bivalent Enhancer	Fetal Brain Male	brain
3	chr5:1930200-1932000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr5:1930400-1931200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
5	chr5:1930400-1931600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:1930400-1931800	Active TSS	Gastric	stomach
7	chr5:1930400-1932200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr5:1930400-1932200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:1930400-1932200	Flanking Active TSS	NHEK	skin
10	chr5:1930400-1932400	Flanking Active TSS	HMEC	breast
11	chr5:1930600-1931200	Active TSS	Brain Anterior Caudate	brain
12	chr5:1930600-1931200	Flanking Active TSS	Esophagus	oesophagus
13	chr5:1930600-1931600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:1930600-1931800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
15	chr5:1930600-1932000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:1930600-1932000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:1930600-1932000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
18	chr5:1930600-1932000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:1930600-1932000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:1930600-1932000	Bivalent/Poised TSS	Fetal Brain Female	brain
21	chr5:1930600-1932000	Active TSS	Rectal Smooth Muscle	rectum
22	chr5:1930600-1932200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr5:1930600-1932200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:1930600-1932400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr5:1930600-1932400	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:1930800-1931200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:1930800-1931600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
28	chr5:1930800-1931600	Bivalent/Poised TSS	Thymus	Thymus
29	chr5:1930800-1931800	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr5:1930800-1931800	Active TSS	Aorta	Aorta
31	chr5:1930800-1931800	Bivalent Enhancer	Placenta	Placenta
32	chr5:1930800-1932000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr5:1930800-1932000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
34	chr5:1930800-1932000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:1930800-1932000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
36	chr5:1930800-1932000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
37	chr5:1930800-1932000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:1930800-1932000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:1930800-1932000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
40	chr5:1930800-1932000	Bivalent/Poised TSS	Fetal Stomach	stomach
41	chr5:1930800-1932000	Active TSS	Psoas Muscle	Psoas
42	chr5:1930800-1932000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
43	chr5:1930800-1932000	Bivalent Enhancer	Spleen	Spleen
44	chr5:1930800-1932200	Active TSS	H9 Cell Line	embryonic stem cell
45	chr5:1930800-1932200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr5:1930800-1932200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:1930800-1932200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
48	chr5:1930800-1932200	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr5:1930800-1932200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr5:1930800-1932200	Active TSS	Colon Smooth Muscle	Colon

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