Variant report

Variant	rs3811749
Chromosome Location	chr4:152329660-152329661
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	MAX	chr4:152329548-152330545	H1-hESC	embryonic stem cell:	n/a	chr4:152330312-152330322 chr4:152329635-152329645
2	EBF1	chr4:152328873-152330169	GM12878	blood:	n/a	n/a
3	MXI1	chr4:152329467-152330495	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr4:152329393-152330474	GM19193	blood:	n/a	n/a
5	BACH1	chr4:152329039-152330143	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr4:152329490-152330650	ECC-1	luminal epithelium:	n/a	chr4:152330312-152330322 chr4:152329635-152329645
7	TAF1	chr4:152329471-152330197	H1-hESC	embryonic stem cell:	n/a	n/a
8	SIN3A	chr4:152328913-152331560	H1-hESC	embryonic stem cell:	n/a	chr4:152330620-152330628 chr4:152330621-152330634
9	POLR2A	chr4:152329344-152331526	Hela-S3	cervix:	n/a	n/a
10	E2F4	chr4:152329653-152330506	MCF10A-Er-Src	breast:	n/a	n/a
11	SIN3AK20	chr4:152329580-152330173	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr4:152329428-152331004	HCT-116	colon:	n/a	chr4:152330312-152330322 chr4:152329635-152329645
13	POLR2A	chr4:152329646-152330626	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr4:152329544-152330173	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAFK	chr4:152329660-152330068	H1-hESC	embryonic stem cell:	n/a	chr4:152329741-152329751 chr4:152329765-152329776 chr4:152329763-152329777 chr4:152329764-152329775 chr4:152329760-152329775 chr4:152329765-152329776 chr4:152329764-152329775
16	POLR2A	chr4:152329643-152330641	MCF-7	breast:	n/a	n/a
17	E2F6	chr4:152329575-152330644	K562	blood:	n/a	n/a
18	POLR2A	chr4:152329638-152330625	MCF-7	breast:	n/a	n/a
19	TCF7L2	chr4:152329641-152330121	Hela-S3	cervix:	n/a	n/a
20	RCOR1	chr4:152329656-152330356	Hela-S3	cervix:	n/a	n/a
21	YY1	chr4:152329055-152329917	H1-hESC	embryonic stem cell:	n/a	chr4:152329302-152329313 chr4:152329244-152329258
22	MYC	chr4:152329620-152330178	H1-hESC	embryonic stem cell:	n/a	chr4:152329635-152329645
23	ELK1	chr4:152329652-152330163	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr4:152329504-152330156	H1-hESC	embryonic stem cell:	n/a	n/a
25	WRNIP1	chr4:152329585-152329740	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:152329625-152330226	ECC-1	luminal epithelium:	n/a	n/a
27	E2F6	chr4:152329253-152330195	H1-hESC	embryonic stem cell:	n/a	n/a
28	ZKSCAN1	chr4:152329588-152330189	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr4:152329443-152331848	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr4:152329442-152330677	H1-hESC	embryonic stem cell:	n/a	n/a
31	SMARCB1	chr4:152329579-152331434	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr4:152329626-152330206	Hela-S3	cervix:	n/a	n/a
33	MAZ	chr4:152329570-152330634	IMR90	lung:	n/a	chr4:152330312-152330322 chr4:152329635-152329645
34	RCOR1	chr4:152328783-152330117	IMR90	lung:	n/a	n/a
35	SMC3	chr4:152329555-152330512	Hela-S3	cervix:	n/a	n/a
36	HEY1	chr4:152329659-152330179	HepG2	liver:	n/a	chr4:152330111-152330126 chr4:152330106-152330121
37	RFX5	chr4:152329575-152330220	Hela-S3	cervix:	n/a	n/a
38	KAP1	chr4:152329572-152330060	HEK293	kidney:	n/a	n/a
39	RAD21	chr4:152329643-152330206	H1-hESC	embryonic stem cell:	n/a	chr4:152329687-152329700 chr4:152329686-152329698
40	EP300	chr4:152329557-152330373	ECC-1	luminal epithelium:	n/a	n/a
41	MAX	chr4:152329655-152330506	HCT-116	colon:	n/a	chr4:152330312-152330322
42	MAX	chr4:152329616-152331459	Hela-S3	cervix:	n/a	chr4:152330312-152330322 chr4:152329635-152329645
43	TCF12	chr4:152329652-152331578	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr4:152329512-152330136	H1-hESC	embryonic stem cell:	n/a	n/a
45	BHLHE40	chr4:152328848-152330160	GM12878	blood:	n/a	chr4:152329357-152329373 chr4:152330106-152330122
46	POLR2A	chr4:152328956-152330792	H1-hESC	embryonic stem cell:	n/a	n/a
47	MXI1	chr4:152329493-152330693	SK-N-SH	brain:	n/a	n/a
48	MAX	chr4:152329158-152330520	HepG2	liver:	n/a	chr4:152329286-152329295 chr4:152330312-152330322 chr4:152329635-152329645
49	SP1	chr4:152329621-152330660	HCT-116	colon:	n/a	n/a
50	RAD21	chr4:152329655-152330192	Hela-S3	cervix:	n/a	chr4:152329687-152329700 chr4:152329686-152329698

No.	Distal block	Cell Line	Cell type
1	chr4:152329542..152330364-chr6:26026932..26027811,2	Hela-S3	cervix:
2	chr4:152019364..152021476-chr4:152328335..152331101,2	MCF-7	breast:
3	chr4:152245112..152247146-chr4:152328940..152330768,2	MCF-7	breast:
4	chr4:152244677..152247078-chr4:152328782..152331586,3	MCF-7	breast:
5	chr1:109288999..109289870-chr4:152329601..152330413,2	Hela-S3	cervix:
6	chr4:152329639..152330392-chr8:130951751..130952461,2	HCT-116	colon:
7	chr1:89149595..89150508-chr4:152329195..152330084,2	Hela-S3	cervix:
8	chr4:152327541..152330018-chr4:152354907..152357662,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH3D19-1	chr4:152326596-152330019	NONHSAT098755

Variant related genes	Relation type
FAM160A1	TF binding region
ENSG00000124529	Chromatin interaction
ENSG00000116266	Chromatin interaction
ENSG00000164142	Chromatin interaction
ENSG00000065243	Chromatin interaction
ENSG00000153310	Chromatin interaction
ENSG00000253720	Chromatin interaction
ENSG00000145425	Chromatin interaction
ENSG00000109686	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10857261	0.84[EUR][1000 genomes]
rs11099804	0.83[EUR][1000 genomes]
rs11099808	0.86[EUR][1000 genomes]
rs11099809	0.86[EUR][1000 genomes]
rs11099810	0.86[EUR][1000 genomes]
rs11099813	0.97[EUR][1000 genomes]
rs11099818	0.86[EUR][1000 genomes]
rs11726171	0.97[EUR][1000 genomes]
rs11726222	0.86[EUR][1000 genomes]
rs11726545	0.84[EUR][1000 genomes]
rs11728501	0.85[EUR][1000 genomes]
rs11728871	0.87[EUR][1000 genomes]
rs11729514	0.86[EUR][1000 genomes]
rs11734176	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11735143	0.86[EUR][1000 genomes]
rs11736261	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11736961	0.92[EUR][1000 genomes]
rs11934818	0.86[EUR][1000 genomes]
rs11947720	0.87[EUR][1000 genomes]
rs12498556	0.92[EUR][1000 genomes]
rs12498878	0.92[EUR][1000 genomes]
rs12499534	0.86[EUR][1000 genomes]
rs12502212	0.86[EUR][1000 genomes]
rs12504273	0.84[EUR][1000 genomes]
rs12508678	0.86[EUR][1000 genomes]
rs1372979	0.84[EUR][1000 genomes]
rs1443085	0.84[EUR][1000 genomes]
rs17275584	0.84[EUR][1000 genomes]
rs1992517	0.86[EUR][1000 genomes]
rs2897619	0.87[EUR][1000 genomes]
rs36083376	0.86[EUR][1000 genomes]
rs3811748	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934474	0.92[EUR][1000 genomes]
rs4371601	0.84[EUR][1000 genomes]
rs4622982	0.85[EUR][1000 genomes]
rs56092201	0.86[EUR][1000 genomes]
rs56763519	0.94[EUR][1000 genomes]
rs57178913	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57272881	0.86[EUR][1000 genomes]
rs57348790	0.96[EUR][1000 genomes]
rs57902858	0.83[EUR][1000 genomes]
rs58863309	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58961701	0.87[EUR][1000 genomes]
rs59097700	0.83[EUR][1000 genomes]
rs59731141	0.86[EUR][1000 genomes]
rs59777523	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59811197	0.85[EUR][1000 genomes]
rs59984665	0.92[EUR][1000 genomes]
rs60055392	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60077220	0.92[EUR][1000 genomes]
rs60169090	0.84[EUR][1000 genomes]
rs60707008	0.92[EUR][1000 genomes]
rs61294884	0.84[EUR][1000 genomes]
rs61302767	0.86[EUR][1000 genomes]
rs61630225	0.80[EUR][1000 genomes]
rs6535791	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6535802	0.92[EUR][1000 genomes]
rs6535805	0.86[EUR][1000 genomes]
rs6813289	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817055	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6826318	0.84[EUR][1000 genomes]
rs6832899	0.84[EUR][1000 genomes]
rs6835310	0.84[EUR][1000 genomes]
rs6838608	0.85[EUR][1000 genomes]
rs6844169	0.86[EUR][1000 genomes]
rs6845067	0.92[EUR][1000 genomes]
rs6846013	0.92[EUR][1000 genomes]
rs6851305	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6853342	0.83[EUR][1000 genomes]
rs6856392	0.82[EUR][1000 genomes]
rs73861275	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73861826	0.89[EUR][1000 genomes]
rs73861827	0.89[EUR][1000 genomes]
rs73862055	0.84[EUR][1000 genomes]
rs73862076	0.81[EUR][1000 genomes]
rs73864013	0.94[EUR][1000 genomes]
rs7653926	0.84[EUR][1000 genomes]
rs7655466	0.84[EUR][1000 genomes]
rs7662214	0.86[EUR][1000 genomes]
rs7662713	0.81[EUR][1000 genomes]
rs7664074	0.86[EUR][1000 genomes]
rs7675933	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7677528	0.92[EUR][1000 genomes]
rs7678496	0.83[EUR][1000 genomes]
rs7684972	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7690773	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9683881	0.97[EUR][1000 genomes]
rs9917912	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1025192	chr4:152202627-152498890	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537307	chr4:152202627-152498890	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv880624	chr4:152280646-152549112	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv822774	chr4:152329489-152330642	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152328600-152329800	Flanking Active TSS	Duodenum Mucosa	Duodenum
2	chr4:152328600-152329800	Flanking Active TSS	GM12878-XiMat	blood
3	chr4:152328600-152329800	Flanking Active TSS	NHEK	skin
4	chr4:152328600-152331400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr4:152328800-152329800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr4:152328800-152329800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr4:152328800-152329800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr4:152328800-152329800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
9	chr4:152328800-152329800	Flanking Active TSS	HMEC	breast
10	chr4:152328800-152330000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
11	chr4:152328800-152330000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
12	chr4:152328800-152330200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:152328800-152331600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr4:152328800-152332000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr4:152329000-152329800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:152329000-152329800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr4:152329000-152329800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:152329000-152329800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:152329000-152329800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
20	chr4:152329000-152329800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr4:152329000-152329800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr4:152329000-152329800	Flanking Active TSS	Hela-S3	cervix
23	chr4:152329000-152329800	Flanking Bivalent TSS/Enh	Osteobl	bone
24	chr4:152329000-152330000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:152329000-152330000	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr4:152329000-152330000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
27	chr4:152329000-152330000	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr4:152329000-152330000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr4:152329000-152330000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr4:152329000-152330000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:152329000-152330000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:152329000-152330000	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr4:152329000-152330000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
34	chr4:152329000-152330200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
35	chr4:152329000-152330200	Flanking Bivalent TSS/Enh	Dnd41	blood
36	chr4:152329000-152330400	Active TSS	Colonic Mucosa	Colon
37	chr4:152329000-152330800	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr4:152329000-152331200	Active TSS	Brain Hippocampus Middle	brain
39	chr4:152329000-152331200	Active TSS	Stomach Mucosa	stomach
40	chr4:152329000-152331400	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr4:152329000-152331400	Active TSS	Fetal Kidney	kidney
42	chr4:152329000-152331600	Active TSS	Gastric	stomach
43	chr4:152329000-152331800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:152329000-152331800	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr4:152329000-152331800	Active TSS	Esophagus	oesophagus
46	chr4:152329000-152332000	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr4:152329000-152333000	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr4:152329200-152329800	Flanking Active TSS	Liver	Liver
49	chr4:152329200-152329800	Enhancers	Fetal Heart	heart
50	chr4:152329200-152329800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle

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