Variant report

Variant	rs250233
Chromosome Location	chr5:50264172-50264173
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	POLR2A	chr5:50261628-50264919	H1-neurons	neurons:	n/a	n/a
2	GATA3	chr5:50263921-50264300	SH-SY5Y	brain:	n/a	chr5:50264176-50264197 chr5:50264179-50264195 chr5:50264183-50264192 chr5:50264183-50264192 chr5:50264164-50264171 chr5:50263968-50263975 chr5:50264179-50264195 chr5:50264182-50264192
3	SUZ12	chr5:50262485-50266469	NT2-D1	testis:	n/a	n/a
4	GATA2	chr5:50263552-50266094	SH-SY5Y	brain:	n/a	chr5:50264176-50264197 chr5:50264179-50264195 chr5:50264183-50264192 chr5:50264183-50264192 chr5:50264164-50264171 chr5:50263968-50263975 chr5:50264179-50264195 chr5:50264859-50264868 chr5:50264182-50264192 chr5:50266034-50266043
5	TCF12	chr5:50263846-50264684	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr5:50261875-50264646	H1-neurons	neurons:	n/a	n/a
7	REST	chr5:50261713-50266474	H1-neurons	neurons:	n/a	chr5:50264435-50264449 chr5:50264118-50264138 chr5:50264118-50264138 chr5:50265442-50265452 chr5:50264121-50264134

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:50264156-50264206	AG10803	skin:	n/a
2	chr5:50264156-50264206	U87	brain:	n/a
3	chr5:50264156-50264206	AG09309	skin:	n/a
4	chr5:50264156-50264206	HRPEpiC	eye:	n/a
5	chr5:50264156-50264206	BE2_C	brain:	n/a
6	chr5:50264156-50264206	NB4	blood:	n/a
7	chr5:50264156-50264206	SK-N-SH	brain:	n/a
8	chr5:50264156-50264206	CMK	blood:	n/a
9	chr5:50264156-50264206	HNPCEpiC	eye:	n/a
10	chr5:50264156-50264206	H1-hESC	embryonic stem cell:	embryo
11	chr5:50264156-50264206	Caco-2	colon:	n/a
12	chr5:50264156-50264206	MCF-7	breast:	n/a
13	chr5:50264156-50264206	SK-N-SH_RA	brain:	n/a
14	chr5:50264156-50264206	GM19239	blood:	n/a
15	chr5:50264156-50264206	IMR90	lung:	fetal
16	chr5:50264156-50264206	HRCEpiC	kidney:	n/a
17	chr5:50264156-50264206	PFSK-1	brain:	n/a
18	chr5:50264156-50264206	ProgFib	skin:	n/a
19	chr5:50264156-50264206	HL-60	blood:	n/a
20	chr5:50264156-50264206	ovcar-3	ovarian:	n/a
21	chr5:50264156-50264206	HMEC	breast:	n/a
22	chr5:50264156-50264206	RPTEC	kidney:	n/a
23	chr5:50264156-50264206	HCF	heart:	n/a
24	chr5:50264156-50264206	HAEpiC	amniotic membrane:	n/a
25	chr5:50264156-50264206	BJ	skin:	n/a
26	chr5:50264156-50264206	GM12892	blood:	n/a
27	chr5:50264156-50264206	K562	blood:	n/a
28	chr5:50264156-50264206	GM06990	blood:	n/a
29	chr5:50264156-50264206	HCPEpiC	choroid plexus:	n/a
30	chr5:50264156-50264206	PrEC	prostate:	n/a
31	chr5:50264156-50264206	HPAEpiC	pulmonary alveolar:	n/a
32	chr5:50264156-50264206	Jurkat	blood:	n/a
33	chr5:50264156-50264206	PANC-1	pancreas:	n/a
34	chr5:50264156-50264206	HepG2	liver:	n/a
35	chr5:50264156-50264206	NHBE	bronchial:	n/a
36	chr5:50264156-50264206	ECC-1	luminal epithelium:	n/a
37	chr5:50264156-50264206	SK-N-MC	brain:	n/a
38	chr5:50264156-50264206	SKMC	muscle:	n/a
39	chr5:50264156-50264206	Hela-S3	cervix:	n/a
40	chr5:50264156-50264206	NH-A	brain:	n/a
41	chr5:50264156-50264206	HCT-116	colon:	n/a
42	chr5:50264156-50264206	HEEpiC	esophagus:	n/a
43	chr5:50264156-50264206	AG09319	gingival:	n/a
44	chr5:50264156-50264206	AG04450	lung:	fetal
45	chr5:50264156-50264206	MCF10A-Er-Src	breast:	n/a
46	chr5:50264156-50264206	T-47D	breast:	n/a
47	chr5:50264156-50264206	HRE	kidney:	n/a
48	chr5:50264156-50264206	AoSMC	blood vessel:	n/a
49	chr5:50264156-50264206	AG04449	skin:	fetal
50	chr5:50264156-50264206	GM12891	blood:	n/a

Variant related genes	Relation type
ENSG00000250360	TF binding region
ENSG00000248918	TF binding region
ENSG00000248918	CpG island
ENSG00000250360	CpG island

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10054384	1.00[ASN][1000 genomes]
rs10472047	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs16887696	1.00[ASN][1000 genomes]
rs16888239	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs185137	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs250236	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs250237	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4626298	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5005508	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55833214	1.00[ASN][1000 genomes]
rs6864779	1.00[ASN][1000 genomes]
rs72758259	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72758263	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72758266	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73752801	0.89[ASN][1000 genomes]
rs7703469	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717928	1.00[ASN][1000 genomes]
rs7725532	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7730386	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv830286	chr5:50165805-50374600	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50258600-50266600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr5:50260200-50265000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:50261400-50266400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr5:50261400-50266400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr5:50261600-50264400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr5:50262200-50264200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr5:50262600-50264200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr5:50262600-50264400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
9	chr5:50262600-50265200	Bivalent/Poised TSS	NHDF-Ad	bronchial
10	chr5:50262600-50266000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
11	chr5:50262600-50266200	Bivalent/Poised TSS	Fetal Stomach	stomach
12	chr5:50262800-50264200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
13	chr5:50262800-50264600	Bivalent/Poised TSS	Thymus	Thymus
14	chr5:50262800-50265200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:50262800-50265200	Bivalent/Poised TSS	Psoas Muscle	Psoas
16	chr5:50262800-50265400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
17	chr5:50262800-50266200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
18	chr5:50263000-50265000	Bivalent/Poised TSS	Left Ventricle	heart
19	chr5:50263000-50265200	Active TSS	Right Atrium	heart
20	chr5:50263000-50266000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
21	chr5:50263000-50266000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
22	chr5:50263200-50265600	Active TSS	Stomach Smooth Muscle	stomach
23	chr5:50263200-50265800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
24	chr5:50263200-50265800	Bivalent Enhancer	Fetal Heart	heart
25	chr5:50263200-50266000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
26	chr5:50263200-50266000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
27	chr5:50263400-50265400	Flanking Bivalent TSS/Enh	Liver	Liver
28	chr5:50263400-50265600	Bivalent/Poised TSS	Aorta	Aorta
29	chr5:50263400-50265800	Bivalent Enhancer	Fetal Brain Male	brain
30	chr5:50263400-50265800	Active TSS	Gastric	stomach
31	chr5:50263400-50266000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:50263600-50264400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr5:50263600-50264400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
34	chr5:50263600-50264400	Bivalent/Poised TSS	Colonic Mucosa	Colon
35	chr5:50263600-50265200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr5:50263600-50266000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr5:50263600-50266000	Bivalent Enhancer	Fetal Lung	lung
38	chr5:50263800-50264200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
39	chr5:50263800-50264200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
40	chr5:50263800-50264200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
41	chr5:50263800-50264400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
42	chr5:50263800-50264400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
43	chr5:50263800-50264600	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:50263800-50264600	Active TSS	Right Ventricle	heart
45	chr5:50263800-50265200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
46	chr5:50263800-50265200	Bivalent Enhancer	Fetal Intestine Small	intestine
47	chr5:50263800-50265200	Enhancers	Pancreas	Pancrea
48	chr5:50263800-50265400	Bivalent Enhancer	Fetal Intestine Large	intestine
49	chr5:50263800-50265600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:50263800-50265600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood

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