Variant report

Variant	rs74018311
Chromosome Location	chr15:55489624-55489625
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	CEBPB	chr15:55488155-55489674	Hela-S3	cervix:	n/a	chr15:55489137-55489148 chr15:55488577-55488590
2	CREB1	chr15:55488819-55489635	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr15:55488329-55489664	HL-60	blood:	n/a	n/a
4	POLR2A	chr15:55488517-55489789	K562	blood:	n/a	n/a
5	EP300	chr15:55488919-55489781	GM12878	blood:	n/a	chr15:55489155-55489162 chr15:55488937-55488953 chr15:55489134-55489148
6	POLR2A	chr15:55488887-55489631	ECC-1	luminal epithelium:	n/a	n/a
7	SIX5	chr15:55488810-55489709	A549	lung:	n/a	chr15:55489330-55489344
8	REST	chr15:55488557-55489626	A549	lung:	n/a	n/a
9	CTCF	chr15:55488647-55489655	GM12878	blood:	n/a	chr15:55489339-55489360 chr15:55489344-55489362 chr15:55489345-55489361
10	ATF3	chr15:55488694-55489633	A549	lung:	n/a	chr15:55488948-55488957
11	HCFC1	chr15:55488672-55489830	K562	blood:	n/a	n/a
12	HA-E2F1	chr15:55488637-55489685	MCF-7	breast:	n/a	chr15:55489286-55489295
13	MAX	chr15:55488612-55489668	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr15:55488692-55489668	GM15510	blood:	n/a	n/a
15	POLR2A	chr15:55488354-55489645	Hela-S3	cervix:	n/a	n/a
16	EP300	chr15:55488887-55489830	GM12878	blood:	n/a	chr15:55489155-55489162 chr15:55488937-55488953 chr15:55489134-55489148
17	POLR2A	chr15:55487585-55489837	MCF10A-Er-Src	breast:	n/a	n/a
18	CTCF	chr15:55489540-55489690	A549	lung:	n/a	n/a
19	POLR2A	chr15:55488856-55489990	HCT-116	colon:	n/a	n/a
20	RUNX3	chr15:55488726-55489830	GM12878	blood:	n/a	n/a
21	CTCF	chr15:55489560-55489710	HAc	cerebellar:	n/a	n/a
22	TAF1	chr15:55488611-55489754	H1-neurons	neurons:	n/a	n/a
23	POLR2A	chr15:55488397-55489650	MCF-7	breast:	n/a	n/a
24	MAZ	chr15:55487989-55489902	K562	blood:	n/a	n/a
25	RELA	chr15:55488657-55489745	GM19099	blood:	n/a	n/a
26	MAFK	chr15:55488354-55489951	Hela-S3	cervix:	n/a	n/a
27	MXI1	chr15:55487285-55490596	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr15:55488316-55489662	GM12878	blood:	n/a	n/a
29	TAF7	chr15:55488639-55489631	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr15:55489600-55489750	NHLF	lung:	n/a	n/a
31	RUNX3	chr15:55488643-55489872	GM12878	blood:	n/a	n/a
32	SP1	chr15:55488769-55489636	A549	lung:	n/a	n/a
33	PML	chr15:55488753-55489633	K562	blood:	n/a	n/a
34	POLR2A	chr15:55488515-55489733	GM12892	blood:	n/a	n/a
35	MAX	chr15:55488656-55489645	MCF-7	breast:	n/a	n/a
36	TAF1	chr15:55488561-55489645	H1-hESC	embryonic stem cell:	n/a	n/a
37	RCOR1	chr15:55488885-55490002	GM12878	blood:	n/a	n/a
38	POU2F2	chr15:55488740-55489644	GM12891	blood:	n/a	n/a
39	CEBPB	chr15:55488398-55489688	A549	lung:	n/a	chr15:55489137-55489148 chr15:55488577-55488590
40	POLR2A	chr15:55488188-55489820	GM12878	blood:	n/a	n/a
41	MAX	chr15:55488489-55489714	HCT-116	colon:	n/a	n/a
42	POLR2A	chr15:55488481-55489956	K562	blood:	n/a	n/a
43	POLR2A	chr15:55488610-55489666	GM19193	blood:	n/a	n/a
44	EBF1	chr15:55488548-55489961	GM12878	blood:	n/a	chr15:55488881-55488892 chr15:55488880-55488893 chr15:55488882-55488892 chr15:55488882-55488891
45	HCFC1	chr15:55488000-55490587	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr15:55488374-55489780	PFSK-1	brain:	n/a	n/a
47	POLR2A	chr15:55488539-55489690	GM18526	blood:	n/a	n/a
48	MAX	chr15:55488552-55489641	SK-N-SH	brain:	n/a	n/a
49	RCOR1	chr15:55487915-55490059	Hela-S3	cervix:	n/a	n/a
50	TEAD4	chr15:55488876-55489661	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:55484699..55490442-chr15:55579270..55584640,8	K562	blood:
2	chr15:55489042..55491644-chr15:55640711..55643190,2	K562	blood:
3	chr15:55488451..55490602-chr15:55640573..55642962,2	MCF-7	breast:
4	chr15:55485508..55492313-chr15:55579801..55583590,12	K562	blood:
5	chr15:55488902..55489642-chr19:33793325..33793871,2	HCT-116	colon:
6	chr15:55489108..55489798-chr16:89626508..89627135,2	NB4	blood:
7	chr15:54266407..54270072-chr15:55486535..55491034,4	MCF-7	breast:
8	chr15:55488918..55489744-chr9:128003531..128004033,2	Hela-S3	cervix:
9	chr11:62608973..62609631-chr15:55489207..55489789,2	Hela-S3	cervix:

Variant related genes	Relation type
RSL24D1	TF binding region
ENSG00000044574	Chromatin interaction
ENSG00000230259	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000239705	Chromatin interaction
ENSG00000069943	Chromatin interaction
ENSG00000260916	Chromatin interaction
ENSG00000245848	Chromatin interaction
ENSG00000267296	Chromatin interaction
ENSG00000167526	Chromatin interaction
ENSG00000069974	Chromatin interaction
ENSG00000259669	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs16953222	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55794742	1.00[AMR][1000 genomes]
rs59982153	1.00[EUR][1000 genomes]
rs60000334	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60105418	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60411614	1.00[EUR][1000 genomes]
rs61191495	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7163785	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7179278	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74015513	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74018308	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74018309	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8040376	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8040489	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043176	chr15:55010228-55563000	Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1039471	chr15:55137606-55552555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 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	chr15:55485600-55490600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:55486600-55490000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr15:55486800-55490000	Active TSS	Psoas Muscle	Psoas
4	chr15:55487000-55489800	Active TSS	Colonic Mucosa	Colon
5	chr15:55487000-55490000	Active TSS	NHLF	lung
6	chr15:55487200-55490000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:55487200-55490200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr15:55487400-55490000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr15:55487400-55490200	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr15:55487400-55490200	Active TSS	Right Atrium	heart
11	chr15:55487600-55490000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:55487600-55490000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:55487600-55490000	Active TSS	Fetal Brain Female	brain
14	chr15:55487600-55490200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:55487600-55490400	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr15:55487800-55489800	Active TSS	Placenta Amnion	Placenta Amnion
17	chr15:55487800-55490000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr15:55487800-55490000	Active TSS	H9 Cell Line	embryonic stem cell
19	chr15:55487800-55490000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:55487800-55490000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:55487800-55490000	Active TSS	Fetal Intestine Small	intestine
22	chr15:55487800-55490000	Active TSS	Ovary	ovary
23	chr15:55487800-55490000	Active TSS	HSMMtube	muscle
24	chr15:55487800-55490200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:55487800-55490200	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr15:55487800-55490200	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr15:55487800-55490200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:55487800-55490200	Active TSS	Right Ventricle	heart
29	chr15:55487800-55490400	Active TSS	K562	blood
30	chr15:55488000-55489800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:55488000-55489800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:55488000-55489800	Active TSS	Muscle Satellite Cultured Cells	--
33	chr15:55488000-55489800	Active TSS	Colon Smooth Muscle	Colon
34	chr15:55488000-55489800	Active TSS	Fetal Thymus	thymus
35	chr15:55488000-55489800	Active TSS	Small Intestine	intestine
36	chr15:55488000-55489800	Active TSS	NHDF-Ad	bronchial
37	chr15:55488000-55490000	Active TSS	H1 Cell Line	embryonic stem cell
38	chr15:55488000-55490000	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr15:55488000-55490000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr15:55488000-55490000	Active TSS	Primary T cells fromperipheralblood	blood
41	chr15:55488000-55490000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:55488000-55490000	Active TSS	Brain Anterior Caudate	brain
43	chr15:55488000-55490000	Active TSS	Fetal Intestine Large	intestine
44	chr15:55488000-55490000	Active TSS	Fetal Muscle Trunk	muscle
45	chr15:55488000-55490000	Active TSS	Left Ventricle	heart
46	chr15:55488000-55490000	Active TSS	HSMM	muscle
47	chr15:55488000-55490000	Active TSS	NH-A	brain
48	chr15:55488000-55490200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:55488000-55490200	Active TSS	Fetal Muscle Leg	muscle
50	chr15:55488000-55490200	Active TSS	GM12878-XiMat	blood

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