Variant report

Variant	rs4252221
Chromosome Location	chr5:68664647-68664648
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	BCL11A	chr5:68664642-68665020	GM12878	blood:	n/a	chr5:68664724-68664733
2	HEY1	chr5:68664290-68666023	HepG2	liver:	n/a	chr5:68665457-68665472
3	POLR2A	chr5:68664385-68666500	GM18505	blood:	n/a	n/a
4	RCOR1	chr5:68664637-68665921	HepG2	liver:	n/a	n/a
5	MYC	chr5:68664313-68665983	NB4	blood:	n/a	chr5:68665348-68665359
6	MXI1	chr5:68664385-68666069	HepG2	liver:	n/a	n/a
7	YY1	chr5:68664583-68666084	GM12878	blood:	n/a	chr5:68665453-68665467 chr5:68665447-68665461
8	CEBPB	chr5:68664343-68664953	K562	blood:	n/a	n/a
9	TCF7L2	chr5:68664392-68665675	PANC-1	pancreas:	n/a	chr5:68664737-68664746 chr5:68664734-68664748 chr5:68664736-68664745 chr5:68664733-68664749 chr5:68664734-68664748 chr5:68664659-68664673 chr5:68664737-68664747 chr5:68664733-68664749
10	MAZ	chr5:68664618-68666180	GM12878	blood:	n/a	chr5:68665348-68665359
11	POLR2A	chr5:68663484-68665983	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr5:68664373-68665914	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr5:68664608-68666177	Raji	blood:	n/a	n/a
14	POLR2A	chr5:68664603-68666089	GM18951	blood:	n/a	n/a
15	CHD1	chr5:68664620-68665300	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr5:68664483-68666118	H1-neurons	neurons:	n/a	n/a
17	HCFC1	chr5:68664542-68665983	K562	blood:	n/a	n/a
18	MYC	chr5:68663507-68666034	K562	blood:	n/a	chr5:68665348-68665359
19	HEY1	chr5:68664526-68665921	HepG2	liver:	n/a	chr5:68665457-68665472
20	POLR2A	chr5:68664497-68665996	GM12891	blood:	n/a	n/a
21	POLR2A	chr5:68664382-68666223	GM12892	blood:	n/a	n/a
22	CEBPD	chr5:68664558-68665913	K562	blood:	n/a	n/a
23	MAX	chr5:68664470-68666079	HepG2	liver:	n/a	chr5:68665348-68665359
24	CHD2	chr5:68664440-68666061	K562	blood:	n/a	n/a
25	RFX5	chr5:68664554-68664973	Hela-S3	cervix:	n/a	n/a
26	MYC	chr5:68664425-68665731	MCF10A-Er-Src	breast:	n/a	chr5:68665348-68665359
27	EP300	chr5:68664332-68665220	K562	blood:	n/a	chr5:68664835-68664849
28	POLR2A	chr5:68664090-68666103	PANC-1	pancreas:	n/a	n/a
29	YY1	chr5:68664566-68665933	K562	blood:	n/a	chr5:68665453-68665467 chr5:68665447-68665461
30	MAX	chr5:68664593-68665928	ECC-1	luminal epithelium:	n/a	chr5:68665348-68665359
31	TCF7L2	chr5:68664551-68665889	HCT-116	colon:	n/a	chr5:68664737-68664746 chr5:68664734-68664748 chr5:68664736-68664745 chr5:68664733-68664749 chr5:68664734-68664748 chr5:68664659-68664673 chr5:68664737-68664747 chr5:68664733-68664749
32	MXI1	chr5:68664623-68666015	GM12878	blood:	n/a	n/a
33	POLR2A	chr5:68664564-68666016	GM12878	blood:	n/a	n/a
34	POLR2A	chr5:68664552-68666204	Hela-S3	cervix:	n/a	n/a
35	BHLHE40	chr5:68664467-68666092	K562	blood:	n/a	chr5:68665349-68665358 chr5:68665349-68665358 chr5:68665343-68665364 chr5:68665347-68665360 chr5:68665350-68665359
36	YY1	chr5:68664526-68665919	GM12878	blood:	n/a	chr5:68665453-68665467 chr5:68665447-68665461
37	POLR2A	chr5:68664474-68666157	HUVEC	blood vessel:	n/a	n/a
38	SIN3AK20	chr5:68664434-68666222	MCF-7	breast:	n/a	n/a
39	POLR2A	chr5:68664397-68665992	GM12891	blood:	n/a	n/a
40	POLR2A	chr5:68664515-68666071	GM12892	blood:	n/a	n/a
41	POLR2A	chr5:68664431-68666274	PFSK-1	brain:	n/a	n/a
42	TCF7L2	chr5:68664527-68665915	Hela-S3	cervix:	n/a	chr5:68664737-68664746 chr5:68664734-68664748 chr5:68664736-68664745 chr5:68664733-68664749 chr5:68664734-68664748 chr5:68664659-68664673 chr5:68664737-68664747 chr5:68664733-68664749
43	POLR2A	chr5:68664237-68666124	K562	blood:	n/a	n/a
44	POLR2A	chr5:68664078-68666233	PANC-1	pancreas:	n/a	n/a
45	TBP	chr5:68664492-68666014	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr5:68664546-68666016	GM12892	blood:	n/a	n/a
47	JUND	chr5:68664383-68666088	K562	blood:	n/a	chr5:68665387-68665396
48	EP300	chr5:68664169-68666008	K562	blood:	n/a	chr5:68664835-68664849
49	POLR2A	chr5:68664460-68666146	K562	blood:	n/a	n/a
50	STAT5A	chr5:68664511-68665964	GM12878	blood:	n/a	chr5:68665549-68665561

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	chr5:68626792..68633026-chr5:68660168..68667090,13	MCF-7	breast:
4	chr5:68644789..68648896-chr5:68660361..68665573,5	K562	blood:
5	chr5:68664076..68666329-chr5:68681503..68684780,3	MCF-7	breast:
6	chr5:68628027..68630302-chr5:68663373..68666765,3	K562	blood:
7	chr5:68618836..68621074-chr5:68663910..68666098,2	MCF-7	breast:
8	chr5:68529171..68532388-chr5:68663415..68666737,3	K562	blood:
9	chr5:68462671..68465247-chr5:68664046..68666511,2	K562	blood:
10	chr5:68484208..68487030-chr5:68662372..68666589,5	K562	blood:
11	chr5:68664280..68666817-chr5:68709824..68711367,2	MCF-7	breast:
12	chr5:68626462..68633259-chr5:68656360..68665608,14	MCF-7	breast:
13	chr5:68529081..68531056-chr5:68663452..68665244,2	MCF-7	breast:
14	chr5:68484557..68486514-chr5:68663480..68665519,2	MCF-7	breast:
15	chr5:68388171..68390847-chr5:68662913..68666552,4	K562	blood:
16	chr5:68485320..68486974-chr5:68663729..68665537,2	MCF-7	breast:
17	chr5:68664038..68667254-chr5:68786797..68789724,5	MCF-7	breast:
18	chr5:68664374..68665890-chr5:68677390..68679995,2	K562	blood:
19	chr5:68628802..68630677-chr5:68662896..68664873,2	K562	blood:
20	chr5:68387450..68391238-chr5:68664593..68668133,5	MCF-7	breast:
21	chr5:68483355..68487362-chr5:68663859..68666403,7	K562	blood:
22	chr5:68461424..68464982-chr5:68663773..68666998,5	K562	blood:

Variant related genes	Relation type
RAD17	TF binding region
TAF9	TF binding region
ENSG00000197822	Chromatin interaction
ENSG00000152939	Chromatin interaction
ENSG00000152942	Chromatin interaction
ENSG00000153044	Chromatin interaction
ENSG00000134057	Chromatin interaction
ENSG00000134058	Chromatin interaction
ENSG00000271045	Chromatin interaction
ENSG00000145740	Chromatin interaction
ENSG00000183323	Chromatin interaction
ENSG00000215006	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	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10940223	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948450	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11948887	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11952246	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11952368	0.81[ASN][1000 genomes]
rs11958576	0.81[ASN][1000 genomes]
rs12516805	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12654780	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655061	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12657358	1.00[ASN][1000 genomes]
rs12658135	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12658657	1.00[ASN][1000 genomes]
rs12659035	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1441800	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236632	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010354	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28544229	0.93[EUR][1000 genomes]
rs28687907	0.90[ASN][1000 genomes]
rs28817404	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756399	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756400	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756402	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4425464	0.96[ASN][1000 genomes]
rs4976195	0.93[ASN][1000 genomes]
rs4976197	1.00[ASN][1000 genomes]
rs6450041	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6870267	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6871685	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891574	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72647235	0.93[ASN][1000 genomes]
rs72647237	0.90[ASN][1000 genomes]
rs7729938	0.81[AMR][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	chr5:68663600-68664800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:68663600-68664800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:68663600-68666600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:68663600-68666600	Active TSS	HSMM	muscle
8	chr5:68663600-68666800	Active TSS	H9 Cell Line	embryonic stem cell
9	chr5:68663600-68666800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:68663600-68667000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr5:68663600-68667600	Active TSS	K562	blood
12	chr5:68663800-68664800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:68663800-68664800	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr5:68663800-68666400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:68663800-68666800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:68663800-68666800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:68663800-68667000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:68664000-68664800	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr5:68664000-68664800	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr5:68664000-68664800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr5:68664000-68664800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr5:68664000-68664800	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr5:68664000-68664800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr5:68664000-68664800	Flanking Active TSS	Rectal Smooth Muscle	rectum
25	chr5:68664000-68664800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr5:68664000-68666400	Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr5:68664000-68666400	Active TSS	HSMMtube	muscle
28	chr5:68664000-68666600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:68664000-68666600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:68664000-68666600	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr5:68664000-68666600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:68664000-68666600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:68664000-68666600	Active TSS	Right Ventricle	heart
34	chr5:68664000-68666600	Active TSS	NHEK	skin
35	chr5:68664000-68666800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:68664000-68666800	Active TSS	Fetal Brain Female	brain
37	chr5:68664000-68667000	Active TSS	H1 Cell Line	embryonic stem cell
38	chr5:68664000-68667000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:68664000-68667000	Active TSS	HMEC	breast
40	chr5:68664000-68667000	Active TSS	NHLF	lung
41	chr5:68664200-68664800	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr5:68664200-68664800	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr5:68664200-68664800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr5:68664200-68664800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr5:68664200-68664800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr5:68664200-68664800	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr5:68664200-68664800	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr5:68664200-68664800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr5:68664200-68665200	Active TSS	Right Atrium	heart
50	chr5:68664200-68666200	Bivalent/Poised TSS	HepG2	liver

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