Variant report

Variant	rs3756399
Chromosome Location	chr5:68665809-68665810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:386)
CpG islands
(count:61)
Chromatin interactive
region (count:28)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:386 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr5:68664806-68665840	A549	lung:	n/a	chr5:68664835-68664849
2	MAX	chr5:68664853-68665811	K562	blood:	n/a	chr5:68665348-68665359
3	TAF7	chr5:68665015-68665850	H1-hESC	embryonic stem cell:	n/a	n/a
4	GTF2F1	chr5:68665161-68665890	H1-hESC	embryonic stem cell:	n/a	n/a
5	HEY1	chr5:68664290-68666023	HepG2	liver:	n/a	chr5:68665457-68665472
6	POLR2A	chr5:68664385-68666500	GM18505	blood:	n/a	n/a
7	RCOR1	chr5:68664637-68665921	HepG2	liver:	n/a	n/a
8	YY1	chr5:68664717-68666088	SK-N-SH	brain:	n/a	chr5:68665453-68665467 chr5:68665447-68665461
9	MYC	chr5:68664313-68665983	NB4	blood:	n/a	chr5:68665348-68665359
10	MYC	chr5:68664899-68665868	K562	blood:	n/a	chr5:68665348-68665359
11	MXI1	chr5:68664385-68666069	HepG2	liver:	n/a	n/a
12	YY1	chr5:68664583-68666084	GM12878	blood:	n/a	chr5:68665453-68665467 chr5:68665447-68665461
13	YY1	chr5:68664734-68665904	ECC-1	luminal epithelium:	n/a	chr5:68665453-68665467 chr5:68665447-68665461
14	SP1	chr5:68664817-68665989	A549	lung:	n/a	chr5:68665595-68665607
15	YY1	chr5:68664729-68665827	GM12891	blood:	n/a	chr5:68665453-68665467 chr5:68665447-68665461
16	TAF1	chr5:68664893-68666009	ECC-1	luminal epithelium:	n/a	n/a
17	MAZ	chr5:68664618-68666180	GM12878	blood:	n/a	chr5:68665348-68665359
18	GABPA	chr5:68664792-68665887	MCF-7	breast:	n/a	n/a
19	POLR2A	chr5:68663484-68665983	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr5:68664871-68666092	GM19193	blood:	n/a	n/a
21	POLR2A	chr5:68664373-68665914	HUVEC	blood vessel:	n/a	n/a
22	BCL3	chr5:68665165-68665828	A549	lung:	n/a	chr5:68665453-68665466 chr5:68665460-68665473 chr5:68665449-68665462
23	POLR2A	chr5:68664608-68666177	Raji	blood:	n/a	n/a
24	POLR2A	chr5:68665099-68665891	HepG2	liver:	n/a	n/a
25	POLR2A	chr5:68664603-68666089	GM18951	blood:	n/a	n/a
26	YY1	chr5:68664684-68665916	H1-hESC	embryonic stem cell:	n/a	chr5:68665453-68665467 chr5:68665447-68665461
27	MXI1	chr5:68665075-68665993	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr5:68664483-68666118	H1-neurons	neurons:	n/a	n/a
29	HCFC1	chr5:68664542-68665983	K562	blood:	n/a	n/a
30	TCF3	chr5:68664994-68665852	GM12878	blood:	n/a	n/a
31	GTF2B	chr5:68665139-68666012	K562	blood:	n/a	n/a
32	MYC	chr5:68663507-68666034	K562	blood:	n/a	chr5:68665348-68665359
33	HEY1	chr5:68664526-68665921	HepG2	liver:	n/a	chr5:68665457-68665472
34	RUNX3	chr5:68664810-68665901	GM12878	blood:	n/a	n/a
35	POLR2A	chr5:68664497-68665996	GM12891	blood:	n/a	n/a
36	SIN3AK20	chr5:68664827-68666168	PANC-1	pancreas:	n/a	n/a
37	POLR2A	chr5:68664943-68665982	SK-N-MC	brain:	n/a	n/a
38	MAX	chr5:68664902-68665962	SK-N-SH	brain:	n/a	chr5:68665348-68665359
39	ZMIZ1	chr5:68664659-68666009	K562	blood:	n/a	n/a
40	MAX	chr5:68664668-68666180	HCT-116	colon:	n/a	chr5:68665348-68665359
41	POLR2A	chr5:68664761-68666261	ProgFib	skin:	n/a	n/a
42	POLR2A	chr5:68664382-68666223	GM12892	blood:	n/a	n/a
43	POLR2A	chr5:68664743-68666010	ECC-1	luminal epithelium:	n/a	n/a
44	CEBPD	chr5:68664558-68665913	K562	blood:	n/a	n/a
45	RELA	chr5:68665203-68665999	GM19193	blood:	n/a	n/a
46	MAX	chr5:68664470-68666079	HepG2	liver:	n/a	chr5:68665348-68665359
47	TAF1	chr5:68665172-68666151	Hela-S3	cervix:	n/a	n/a
48	CHD2	chr5:68664440-68666061	K562	blood:	n/a	n/a
49	RPC155	chr5:68665808-68666738	Hela-S3	cervix:	n/a	n/a
50	EP300	chr5:68665349-68665877	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:68665773-68665823	HNPCEpiC	eye:	n/a
2	chr5:68665773-68665823	ovcar-3	ovarian:	n/a
3	chr5:68665773-68665823	HCF	heart:	n/a
4	chr5:68665773-68665823	MCF10A-Er-Src	breast:	n/a
5	chr5:68665773-68665823	GM12878	blood:	n/a
6	chr5:68665773-68665823	SKMC	muscle:	n/a
7	chr5:68665773-68665823	NB4	blood:	n/a
8	chr5:68665773-68665823	AoSMC	blood vessel:	n/a
9	chr5:68665773-68665823	SK-N-SH_RA	brain:	n/a
10	chr5:68665773-68665823	AG09309	skin:	n/a
11	chr5:68665773-68665823	A549	lung:	n/a
12	chr5:68665773-68665823	HEEpiC	esophagus:	n/a
13	chr5:68665773-68665823	GM06990	blood:	n/a
14	chr5:68665773-68665823	HUVEC	blood vessel:	n/a
15	chr5:68665773-68665823	GM12891	blood:	n/a
16	chr5:68665773-68665823	AG09319	gingival:	n/a
17	chr5:68665773-68665823	HRCEpiC	kidney:	n/a
18	chr5:68665773-68665823	IMR90	lung:	fetal
19	chr5:68665773-68665823	SK-N-SH	brain:	n/a
20	chr5:68665773-68665823	HRPEpiC	eye:	n/a
21	chr5:68665773-68665823	RPTEC	kidney:	n/a
22	chr5:68665773-68665823	PANC-1	pancreas:	n/a
23	chr5:68665773-68665823	HAEpiC	amniotic membrane:	n/a
24	chr5:68665773-68665823	NHDF-neo	bronchial:	n/a
25	chr5:68665773-68665823	AG04449	skin:	fetal
26	chr5:68665773-68665823	K562	blood:	n/a
27	chr5:68665773-68665823	HIPEpiC	eye:	n/a
28	chr5:68665773-68665823	HCT-116	colon:	n/a
29	chr5:68665773-68665823	ECC-1	luminal epithelium:	n/a
30	chr5:68665773-68665823	HCPEpiC	choroid plexus:	n/a
31	chr5:68665773-68665823	NHBE	bronchial:	n/a
32	chr5:68665773-68665823	BJ	skin:	n/a
33	chr5:68665773-68665823	HRE	kidney:	n/a
34	chr5:68665773-68665823	Hela-S3	cervix:	n/a
35	chr5:68665773-68665823	Jurkat	blood:	n/a
36	chr5:68665773-68665823	LNCaP	prostate:	n/a
37	chr5:68665773-68665823	PFSK-1	brain:	n/a
38	chr5:68665773-68665823	AG04450	lung:	fetal
39	chr5:68665773-68665823	BE2_C	brain:	n/a
40	chr5:68665773-68665823	H1-hESC	embryonic stem cell:	embryo
41	chr5:68665773-68665823	GM19239	blood:	n/a
42	chr5:68665773-68665823	HEK293	kidney:	embryo
43	chr5:68665773-68665823	HepG2	liver:	n/a
44	chr5:68665773-68665823	NH-A	brain:	n/a
45	chr5:68665773-68665823	Caco-2	colon:	n/a
46	chr5:68665773-68665823	PrEC	prostate:	n/a
47	chr5:68665773-68665823	SK-N-MC	brain:	n/a
48	chr5:68665773-68665823	HPAEpiC	pulmonary alveolar:	n/a
49	chr5:68665773-68665823	HCM	heart:	n/a
50	chr5:68665773-68665823	Hepatocyte	liver:	n/a

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:68388226..68392530-chr5:68662317..68667070,8	K562	blood:
2	chr5:68664291..68666075-chr5:68709843..68712396,3	MCF-7	breast:
3	chr5:68665165..68667031-chr5:68713831..68715758,2	K562	blood:
4	chr5:68461677..68464671-chr5:68665186..68667008,2	MCF-7	breast:
5	chr5:68513382..68515686-chr5:68665012..68667135,2	K562	blood:
6	chr5:68626792..68633026-chr5:68660168..68667090,13	MCF-7	breast:
7	chr5:68664076..68666329-chr5:68681503..68684780,3	MCF-7	breast:
8	chr14:24583442..24584438-chr5:68665005..68665960,2	Hela-S3	cervix:
9	chr15:45694132..45694822-chr5:68665207..68665996,2	HCT-116	colon:
10	chr5:68628027..68630302-chr5:68663373..68666765,3	K562	blood:
11	chr1:45186886..45187775-chr5:68664862..68666137,3	Hela-S3	cervix:
12	chr5:68618836..68621074-chr5:68663910..68666098,2	MCF-7	breast:
13	chr5:68529171..68532388-chr5:68663415..68666737,3	K562	blood:
14	chr5:68462671..68465247-chr5:68664046..68666511,2	K562	blood:
15	chr5:68484208..68487030-chr5:68662372..68666589,5	K562	blood:
16	chr12:54069435..54070055-chr5:68665548..68666271,2	Hela-S3	cervix:
17	chr5:68512009..68514181-chr5:68664891..68666779,2	MCF-7	breast:
18	chr5:68664280..68666817-chr5:68709824..68711367,2	MCF-7	breast:
19	chr19:49122220..49122731-chr5:68664968..68665867,2	Hela-S3	cervix:
20	chr5:68388171..68390847-chr5:68662913..68666552,4	K562	blood:
21	chr5:68664038..68667254-chr5:68786797..68789724,5	MCF-7	breast:
22	chr5:68664374..68665890-chr5:68677390..68679995,2	K562	blood:
23	chr19:58898429..58899151-chr5:68665264..68665895,2	HCT-116	colon:
24	chr5:68387450..68391238-chr5:68664593..68668133,5	MCF-7	breast:
25	chr5:68483355..68487362-chr5:68663859..68666403,7	K562	blood:
26	chr5:68461424..68464982-chr5:68663773..68666998,5	K562	blood:
27	chr5:68665412..68666024-chr5:68787946..68788690,2	MCF-7	breast:
28	chr5:68664964..68667137-chr5:68679012..68681522,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MARVELD2-2	chr5:68665645-68666111	NONHSAT101918

No data

Variant related genes	Relation type
RAD17	TF binding region
TAF9	TF binding region
RAD17	CpG island
TAF9	CpG island
ENSG00000145740	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000171763	Chromatin interaction
ENSG00000129535	Chromatin interaction
ENSG00000171766	Chromatin interaction
ENSG00000153044	Chromatin interaction
ENSG00000183323	Chromatin interaction
ENSG00000134056	Chromatin interaction
ENSG00000063176	Chromatin interaction
ENSG00000215006	Chromatin interaction
ENSG00000100897	Chromatin interaction
ENSG00000135390	Chromatin interaction
ENSG00000152942	Chromatin interaction
ENSG00000083845	Chromatin interaction
ENSG00000152939	Chromatin interaction
ENSG00000134057	Chromatin interaction
ENSG00000063177	Chromatin interaction
ENSG00000134058	Chromatin interaction
ENSG00000197822	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1006633	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10940223	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948450	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11948887	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11952246	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11952368	0.81[ASN][1000 genomes]
rs11958576	0.81[ASN][1000 genomes]
rs12516805	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12654780	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655061	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12657358	1.00[ASN][1000 genomes]
rs12658135	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12658657	1.00[ASN][1000 genomes]
rs12659035	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1441800	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236632	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010354	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28544229	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs28687907	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28817404	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756400	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756402	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4252221	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4425464	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4976195	0.93[ASN][1000 genomes]
rs4976197	1.00[ASN][1000 genomes]
rs6450041	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6870267	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6871685	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891574	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72647235	0.93[ASN][1000 genomes]
rs72647237	0.90[ASN][1000 genomes]
rs7729938	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7730405	0.83[ASN][1000 genomes]
rs7730569	0.83[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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv881767	chr5:68625786-68733698	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68663400-68666600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr5:68663400-68667800	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr5:68663400-68667800	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr5:68663600-68666600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:68663600-68666600	Active TSS	HSMM	muscle
6	chr5:68663600-68666800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr5:68663600-68666800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:68663600-68667000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr5:68663600-68667600	Active TSS	K562	blood
10	chr5:68663800-68666400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:68663800-68666800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:68663800-68666800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:68663800-68667000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:68664000-68666400	Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr5:68664000-68666400	Active TSS	HSMMtube	muscle
16	chr5:68664000-68666600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:68664000-68666600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:68664000-68666600	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr5:68664000-68666600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:68664000-68666600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:68664000-68666600	Active TSS	Right Ventricle	heart
22	chr5:68664000-68666600	Active TSS	NHEK	skin
23	chr5:68664000-68666800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:68664000-68666800	Active TSS	Fetal Brain Female	brain
25	chr5:68664000-68667000	Active TSS	H1 Cell Line	embryonic stem cell
26	chr5:68664000-68667000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:68664000-68667000	Active TSS	HMEC	breast
28	chr5:68664000-68667000	Active TSS	NHLF	lung
29	chr5:68664200-68666200	Bivalent/Poised TSS	HepG2	liver
30	chr5:68664200-68666400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:68664200-68666400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:68664200-68666400	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr5:68664200-68666400	Active TSS	Fetal Intestine Large	intestine
34	chr5:68664200-68666400	Active TSS	Fetal Muscle Leg	muscle
35	chr5:68664200-68666400	Active TSS	Fetal Stomach	stomach
36	chr5:68664200-68666600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:68664200-68666600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:68664200-68666600	Active TSS	Fetal Kidney	kidney
39	chr5:68664200-68666600	Active TSS	Fetal Muscle Trunk	muscle
40	chr5:68664200-68666600	Active TSS	Left Ventricle	heart
41	chr5:68664200-68666600	Active TSS	Ovary	ovary
42	chr5:68664200-68666600	Active TSS	Stomach Mucosa	stomach
43	chr5:68664200-68666600	Active TSS	A549	lung
44	chr5:68664200-68666600	Active TSS	NHDF-Ad	bronchial
45	chr5:68664200-68666800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:68664200-68666800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr5:68664200-68666800	Active TSS	Muscle Satellite Cultured Cells	--
48	chr5:68664200-68666800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr5:68664200-68666800	Active TSS	Psoas Muscle	Psoas
50	chr5:68664200-68667000	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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