Variant report

Variant	rs3756402
Chromosome Location	chr5:68664515-68664516
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	HEY1	chr5:68664290-68666023	HepG2	liver:	n/a	chr5:68665457-68665472
2	POLR2A	chr5:68664385-68666500	GM18505	blood:	n/a	n/a
3	MYC	chr5:68664313-68665983	NB4	blood:	n/a	chr5:68665348-68665359
4	MXI1	chr5:68664385-68666069	HepG2	liver:	n/a	n/a
5	CEBPB	chr5:68664343-68664953	K562	blood:	n/a	n/a
6	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
7	POLR2A	chr5:68663484-68665983	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr5:68664373-68665914	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr5:68664483-68666118	H1-neurons	neurons:	n/a	n/a
10	MYC	chr5:68663507-68666034	K562	blood:	n/a	chr5:68665348-68665359
11	POLR2A	chr5:68664497-68665996	GM12891	blood:	n/a	n/a
12	POLR2A	chr5:68664382-68666223	GM12892	blood:	n/a	n/a
13	MAX	chr5:68664470-68666079	HepG2	liver:	n/a	chr5:68665348-68665359
14	CHD2	chr5:68664440-68666061	K562	blood:	n/a	n/a
15	FOS	chr5:68664458-68664605	MCF10A-Er-Src	breast:	n/a	n/a
16	MYC	chr5:68664425-68665731	MCF10A-Er-Src	breast:	n/a	chr5:68665348-68665359
17	EP300	chr5:68664332-68665220	K562	blood:	n/a	chr5:68664835-68664849
18	POLR2A	chr5:68664090-68666103	PANC-1	pancreas:	n/a	n/a
19	BHLHE40	chr5:68664467-68666092	K562	blood:	n/a	chr5:68665349-68665358 chr5:68665349-68665358 chr5:68665343-68665364 chr5:68665347-68665360 chr5:68665350-68665359
20	POLR2A	chr5:68664474-68666157	HUVEC	blood vessel:	n/a	n/a
21	SIN3AK20	chr5:68664434-68666222	MCF-7	breast:	n/a	n/a
22	POLR2A	chr5:68664397-68665992	GM12891	blood:	n/a	n/a
23	POLR2A	chr5:68664515-68666071	GM12892	blood:	n/a	n/a
24	POLR2A	chr5:68664431-68666274	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr5:68664237-68666124	K562	blood:	n/a	n/a
26	POLR2A	chr5:68664078-68666233	PANC-1	pancreas:	n/a	n/a
27	TBP	chr5:68664492-68666014	H1-hESC	embryonic stem cell:	n/a	n/a
28	JUND	chr5:68664383-68666088	K562	blood:	n/a	chr5:68665387-68665396
29	EP300	chr5:68664169-68666008	K562	blood:	n/a	chr5:68664835-68664849
30	POLR2A	chr5:68664460-68666146	K562	blood:	n/a	n/a
31	STAT5A	chr5:68664511-68665964	GM12878	blood:	n/a	chr5:68665549-68665561
32	MYC	chr5:68664361-68665944	A549	lung:	n/a	chr5:68665348-68665359
33	POLR2A	chr5:68663447-68666118	HepG2	liver:	n/a	n/a
34	POLR2A	chr5:68664458-68666058	GM12891	blood:	n/a	n/a
35	MXI1	chr5:68663590-68666253	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr5:68664393-68666115	SK-N-SH	brain:	n/a	n/a
37	TAL1	chr5:68664005-68666076	K562	blood:	n/a	chr5:68664173-68664181
38	POLR2A	chr5:68664504-68666115	H1-neurons	neurons:	n/a	n/a
39	POLR2A	chr5:68664281-68664605	HepG2	liver:	n/a	n/a
40	SIN3A	chr5:68664242-68666191	H1-hESC	embryonic stem cell:	n/a	chr5:68665458-68665469
41	MYC	chr5:68663526-68666023	K562	blood:	n/a	chr5:68665348-68665359
42	MAFK	chr5:68664499-68664930	Hela-S3	cervix:	n/a	chr5:68664615-68664626
43	TBL1XR1	chr5:68664497-68666070	K562	blood:	n/a	n/a
44	TRIM28	chr5:68664495-68666077	K562	blood:	n/a	n/a
45	MXI1	chr5:68664305-68666110	IMR90	lung:	n/a	n/a
46	JUN	chr5:68664353-68664918	HepG2	liver:	n/a	n/a
47	POLR2A	chr5:68664265-68666085	K562	blood:	n/a	n/a
48	CREB1	chr5:68664459-68665975	K562	blood:	n/a	n/a
49	POLR2A	chr5:68663482-68666039	K562	blood:	n/a	n/a
50	TEAD4	chr5:68664109-68666205	K562	blood:	n/a	n/a

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	chr5:68483355..68487362-chr5:68663859..68666403,7	K562	blood:
21	chr5:68461424..68464982-chr5:68663773..68666998,5	K562	blood:

Variant related genes	Relation type
TAF9	TF binding region
RAD17	TF binding region
ENSG00000152942	Chromatin interaction
ENSG00000271045	Chromatin interaction
ENSG00000197822	Chromatin interaction
ENSG00000152939	Chromatin interaction
ENSG00000215006	Chromatin interaction
ENSG00000153044	Chromatin interaction
ENSG00000134058	Chromatin interaction
ENSG00000134057	Chromatin interaction
ENSG00000145740	Chromatin interaction
ENSG00000183323	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	0.92[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]
rs4252221	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	0.86[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	chr5:68653200-68664600	Weak transcription	Esophagus	oesophagus
2	chr5:68663400-68664600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr5:68663400-68666600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr5:68663400-68667800	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr5:68663400-68667800	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr5:68663600-68664600	Weak transcription	Small Intestine	intestine
7	chr5:68663600-68664800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:68663600-68664800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:68663600-68666600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:68663600-68666600	Active TSS	HSMM	muscle
11	chr5:68663600-68666800	Active TSS	H9 Cell Line	embryonic stem cell
12	chr5:68663600-68666800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:68663600-68667000	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr5:68663600-68667600	Active TSS	K562	blood
15	chr5:68663800-68664600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:68663800-68664600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:68663800-68664600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr5:68663800-68664600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr5:68663800-68664600	Weak transcription	Pancreas	Pancrea
20	chr5:68663800-68664600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:68663800-68664600	Weak transcription	Spleen	Spleen
22	chr5:68663800-68664600	Flanking Active TSS	HUVEC	blood vessel
23	chr5:68663800-68664800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:68663800-68664800	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr5:68663800-68666400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:68663800-68666800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr5:68663800-68666800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:68663800-68667000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:68664000-68664600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr5:68664000-68664600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr5:68664000-68664600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr5:68664000-68664600	Flanking Active TSS	Liver	Liver
33	chr5:68664000-68664600	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr5:68664000-68664600	Flanking Active TSS	Brain Germinal Matrix	brain
35	chr5:68664000-68664600	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr5:68664000-68664600	Flanking Active TSS	Fetal Heart	heart
37	chr5:68664000-68664600	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr5:68664000-68664800	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr5:68664000-68664800	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr5:68664000-68664800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr5:68664000-68664800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr5:68664000-68664800	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr5:68664000-68664800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr5:68664000-68664800	Flanking Active TSS	Rectal Smooth Muscle	rectum
45	chr5:68664000-68664800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr5:68664000-68666400	Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr5:68664000-68666400	Active TSS	HSMMtube	muscle
48	chr5:68664000-68666600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:68664000-68666600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:68664000-68666600	Active TSS	Breast Myoepithelial Primary Cells	Breast

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