Variant report

Variant	rs10038757
Chromosome Location	chr5:75380320-75380321
allele	C/T
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	EGR1	chr5:75380253-75380418	GM12878	blood:	n/a	n/a
2	MAX	chr5:75379811-75380680	H1-hESC	embryonic stem cell:	n/a	n/a
3	EGR1	chr5:75380271-75380460	GM12878	blood:	n/a	n/a
4	EGR1	chr5:75380183-75380550	K562	blood:	n/a	n/a
5	RAD21	chr5:75380252-75380598	SK-N-SH_RA	brain:	n/a	n/a
6	CREB1	chr5:75380243-75380761	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr5:75380257-75380555	SK-N-SH_RA	brain:	n/a	n/a
8	E2F6	chr5:75378885-75380376	H1-hESC	embryonic stem cell:	n/a	chr5:75378949-75378958 chr5:75379166-75379173 chr5:75379514-75379521 chr5:75379165-75379173 chr5:75378946-75378958 chr5:75379269-75379279 chr5:75379165-75379177 chr5:75379166-75379173 chr5:75379723-75379732 chr5:75379166-75379173
9	CTCF	chr5:75380320-75380470	SK-N-SH_RA	brain:	n/a	n/a
10	GATA2	chr5:75378706-75381050	SH-SY5Y	brain:	n/a	chr5:75379607-75379624 chr5:75380885-75380892
11	MXI1	chr5:75377350-75381483	SK-N-SH	brain:	n/a	n/a
12	EGR1	chr5:75380148-75380589	ECC-1	luminal epithelium:	n/a	n/a
13	BACH1	chr5:75380053-75380336	H1-hESC	embryonic stem cell:	n/a	n/a
14	REST	chr5:75378804-75381204	H1-neurons	neurons:	n/a	chr5:75379412-75379422 chr5:75379090-75379103 chr5:75379098-75379118 chr5:75379098-75379112 chr5:75379100-75379110 chr5:75379099-75379117 chr5:75379102-75379115 chr5:75380733-75380746
15	POLR2A	chr5:75379740-75381124	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr5:75378454-75381515	H1-neurons	neurons:	n/a	n/a
17	CTBP2	chr5:75378607-75380344	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:75380303-75380353	LNCaP	prostate:	n/a
2	chr5:75380303-75380353	NHBE	bronchial:	n/a
3	chr5:75380303-75380353	PrEC	prostate:	n/a
4	chr5:75380303-75380353	HCF	heart:	n/a
5	chr5:75380303-75380353	HRPEpiC	eye:	n/a
6	chr5:75380303-75380353	NHDF-neo	bronchial:	n/a
7	chr5:75380303-75380353	NT2-D1	testis:	n/a
8	chr5:75380303-75380353	AoSMC	blood vessel:	n/a
9	chr5:75380303-75380353	AG04449	skin:	fetal
10	chr5:75380303-75380353	AG10803	skin:	n/a
11	chr5:75380303-75380353	SAEC	small airway:	n/a
12	chr5:75380303-75380353	GM12892	blood:	n/a
13	chr5:75380303-75380353	HNPCEpiC	eye:	n/a
14	chr5:75380303-75380353	IMR90	lung:	fetal
15	chr5:75380303-75380353	MCF10A-Er-Src	breast:	n/a
16	chr5:75380303-75380353	CMK	blood:	n/a
17	chr5:75380303-75380353	AG09309	skin:	n/a
18	chr5:75380303-75380353	HPAEpiC	pulmonary alveolar:	n/a
19	chr5:75380303-75380353	PFSK-1	brain:	n/a
20	chr5:75380303-75380353	HCT-116	colon:	n/a
21	chr5:75380303-75380353	H1-hESC	embryonic stem cell:	embryo
22	chr5:75380303-75380353	NH-A	brain:	n/a
23	chr5:75380303-75380353	RPTEC	kidney:	n/a
24	chr5:75380303-75380353	GM12878	blood:	n/a
25	chr5:75380303-75380353	GM06990	blood:	n/a
26	chr5:75380303-75380353	ovcar-3	ovarian:	n/a
27	chr5:75380303-75380353	HCM	heart:	n/a
28	chr5:75380303-75380353	HRE	kidney:	n/a
29	chr5:75380303-75380353	HEEpiC	esophagus:	n/a
30	chr5:75380303-75380353	HMEC	breast:	n/a
31	chr5:75380303-75380353	SK-N-MC	brain:	n/a
32	chr5:75380303-75380353	HepG2	liver:	n/a
33	chr5:75380303-75380353	HIPEpiC	eye:	n/a
34	chr5:75380303-75380353	Hepatocyte	liver:	n/a
35	chr5:75380303-75380353	BE2_C	brain:	n/a
36	chr5:75380303-75380353	Hela-S3	cervix:	n/a
37	chr5:75380303-75380353	A549	lung:	n/a
38	chr5:75380303-75380353	U87	brain:	n/a
39	chr5:75380303-75380353	PANC-1	pancreas:	n/a
40	chr5:75380303-75380353	SKMC	muscle:	n/a
41	chr5:75380303-75380353	NB4	blood:	n/a
42	chr5:75380303-75380353	K562	blood:	n/a
43	chr5:75380303-75380353	SK-N-SH_RA	brain:	n/a
44	chr5:75380303-75380353	ECC-1	luminal epithelium:	n/a
45	chr5:75380303-75380353	GM12891	blood:	n/a
46	chr5:75380303-75380353	HL-60	blood:	n/a
47	chr5:75380303-75380353	GM19239	blood:	n/a
48	chr5:75380303-75380353	HUVEC	blood vessel:	n/a
49	chr5:75380303-75380353	Caco-2	colon:	n/a
50	chr5:75380303-75380353	AG04450	lung:	fetal

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75378752..75382586-chr5:75384314..75388337,4	K562	blood:

Variant related genes	Relation type
ENSG00000248127	TF binding region
ENSG00000248127	CpG island
ENSG00000252833	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10038280	0.94[EUR][1000 genomes]
rs10043369	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10050813	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10054931	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10063621	0.95[EUR][1000 genomes]
rs10064145	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10065114	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10474460	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12513411	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12513447	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12656979	0.89[EUR][1000 genomes]
rs12659929	0.86[ASN][1000 genomes]
rs13160383	0.84[ASN][1000 genomes]
rs1553311	0.89[EUR][1000 genomes]
rs17673786	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17746749	0.96[EUR][1000 genomes]
rs1862520	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28554027	0.88[EUR][1000 genomes]
rs6453199	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7448740	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs767590	0.96[EUR][1000 genomes]
rs7700761	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7702044	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7711218	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7712198	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7725280	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9293666	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9293667	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv869885	chr5:75365786-75419656	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1033350	chr5:75367809-75538460	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 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	chr5:75377400-75381400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
2	chr5:75377600-75381000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr5:75377600-75381000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr5:75377600-75381200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr5:75377600-75381400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr5:75377600-75381600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr5:75377800-75380400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:75377800-75380400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:75377800-75381000	Bivalent Enhancer	Liver	Liver
10	chr5:75377800-75381200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
11	chr5:75377800-75381200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:75377800-75381200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:75378000-75380400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
14	chr5:75378000-75380400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
15	chr5:75378000-75380400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:75378000-75381200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:75378600-75380400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
18	chr5:75378600-75380400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
19	chr5:75378600-75380400	Bivalent Enhancer	Placenta	Placenta
20	chr5:75378800-75380400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:75378800-75380400	Bivalent Enhancer	Spleen	Spleen
22	chr5:75378800-75380800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr5:75378800-75381000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:75378800-75381000	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:75378800-75381000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
26	chr5:75378800-75381200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
27	chr5:75378800-75381200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
28	chr5:75378800-75381200	Active TSS	Rectal Smooth Muscle	rectum
29	chr5:75378800-75381600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
30	chr5:75379000-75380400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
31	chr5:75379000-75381000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr5:75379200-75380400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:75379200-75380800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
34	chr5:75379200-75381000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
35	chr5:75379400-75380400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
36	chr5:75379400-75380400	Bivalent Enhancer	Fetal Thymus	thymus
37	chr5:75379400-75381000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:75379400-75381000	Enhancers	Pancreas	Pancrea
39	chr5:75379400-75381200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
40	chr5:75379400-75381200	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr5:75379400-75381200	Bivalent Enhancer	Lung	lung
42	chr5:75379600-75380400	Bivalent Enhancer	Adipose Nuclei	Adipose
43	chr5:75379600-75380400	Bivalent Enhancer	Brain Substantia Nigra	brain
44	chr5:75379600-75380600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:75379600-75380600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr5:75379600-75380600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr5:75379600-75380800	Bivalent Enhancer	Primary B cells from cord blood	blood
48	chr5:75379600-75381000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:75379600-75381200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
50	chr5:75379800-75380400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle

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