Variant report

Variant	rs554804104
Chromosome Location	chr15:75248724-75248725
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:395)
CpG islands
(count:0)
Chromatin interactive
region (count:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:395 , 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	CTCF	chr15:75248600-75248750	SK-N-SH_RA	brain:	n/a	n/a
2	PML	chr15:75248585-75249759	MCF-7	breast:	n/a	n/a
3	EGR1	chr15:75248435-75248786	K562	blood:	n/a	n/a
4	CTCF	chr15:75248580-75248730	HBMEC	blood vessel:	n/a	n/a
5	CHD2	chr15:75248456-75249959	Hela-S3	cervix:	n/a	n/a
6	GTF2F1	chr15:75248459-75249310	K562	blood:	n/a	n/a
7	JUND	chr15:75248494-75248834	K562	blood:	n/a	n/a
8	SIX5	chr15:75248508-75248737	K562	blood:	n/a	n/a
9	CTCF	chr15:75248580-75248730	GM12865	blood:	n/a	n/a
10	CTCF	chr15:75248700-75248850	RPTEC	kidney:	n/a	n/a
11	SMC3	chr15:75248388-75248867	Hela-S3	cervix:	n/a	n/a
12	JUND	chr15:75248503-75249983	A549	lung:	n/a	n/a
13	CTCF	chr15:75248720-75248870	A549	lung:	n/a	n/a
14	CTCF	chr15:75248580-75248730	HMEC	breast:	n/a	n/a
15	CTCF	chr15:75248580-75248730	HMF	breast:	n/a	n/a
16	RCOR1	chr15:75248427-75248994	K562	blood:	n/a	n/a
17	CTCF	chr15:75248680-75248830	NHDF-neo	bronchial:	n/a	n/a
18	POLR2A	chr15:75248586-75249282	GM12892	blood:	n/a	n/a
19	MYC	chr15:75248423-75249695	K562	blood:	n/a	n/a
20	ATF3	chr15:75248500-75248870	GM12878	blood:	n/a	n/a
21	CTCF	chr15:75248564-75248762	H1-hESC	embryonic stem cell:	n/a	n/a
22	YY1	chr15:75248491-75250071	A549	lung:	n/a	n/a
23	CTCF	chr15:75248640-75248790	HFF-Myc	foreskin:	n/a	n/a
24	CTCF	chr15:75248528-75248830	Spleen_OC	spleen:	n/a	n/a
25	POLR2A	chr15:75248584-75249624	K562	blood:	n/a	n/a
26	CTCF	chr15:75248506-75248833	K562	blood:	n/a	n/a
27	MTA3	chr15:75248346-75248880	GM12878	blood:	n/a	n/a
28	CTCF	chr15:75248535-75248795	GM12892	blood:	n/a	n/a
29	CTCF	chr15:75248640-75248790	NHLF	lung:	n/a	n/a
30	CTCF	chr15:75248580-75248730	HUVEC	blood vessel:	n/a	n/a
31	CTCF	chr15:75248580-75248730	K562	blood:	n/a	n/a
32	CTCF	chr15:75248484-75248803	SK-N-SH_RA	brain:	n/a	n/a
33	CTCF	chr15:75248600-75248750	GM12874	blood:	n/a	n/a
34	CTCF	chr15:75248531-75248796	Pancreas_OC	pancreas:	n/a	n/a
35	USF1	chr15:75248473-75248954	SK-N-SH	brain:	n/a	n/a
36	HDAC2	chr15:75248286-75248876	K562	blood:	n/a	n/a
37	TCF12	chr15:75248153-75250346	A549	lung:	n/a	n/a
38	MXI1	chr15:75246247-75250049	SK-N-SH	brain:	n/a	n/a
39	EGR1	chr15:75248437-75248782	K562	blood:	n/a	n/a
40	CHD2	chr15:75248511-75248806	H1-hESC	embryonic stem cell:	n/a	n/a
41	TBP	chr15:75248421-75249952	H1-hESC	embryonic stem cell:	n/a	n/a
42	MYC	chr15:75248408-75249136	K562	blood:	n/a	n/a
43	POLR2A	chr15:75246125-75250279	SK-N-MC	brain:	n/a	n/a
44	POLR2A	chr15:75247844-75251217	Hela-S3	cervix:	n/a	n/a
45	MYC	chr15:75248491-75248798	Hela-S3	cervix:	n/a	n/a
46	MAX	chr15:75248121-75250119	H1-hESC	embryonic stem cell:	n/a	chr15:75249898-75249908
47	CTCF	chr15:75248580-75248730	AG04450	lung:	n/a	n/a
48	MAX	chr15:75248352-75249966	SK-N-SH	brain:	n/a	chr15:75249898-75249908
49	MYC	chr15:75248535-75248901	MCF-7	breast:	n/a	n/a
50	TCF7L2	chr15:75248412-75249102	PANC-1	pancreas:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:75248197..75251380-chr15:75494107..75498676,4	MCF-7	breast:
2	chr11:61734252..61735028-chr15:75248615..75249148,2	Hela-S3	cervix:
3	chr15:75228700..75232954-chr15:75245461..75250546,13	K562	blood:
4	chr15:75133947..75135664-chr15:75246136..75249268,3	MCF-7	breast:
5	chr15:74906365..74908963-chr15:75246374..75249056,3	MCF-7	breast:
6	chr15:75155291..75158241-chr15:75246616..75248751,2	K562	blood:
7	chr15:75246590..75249281-chr15:75285572..75288569,4	MCF-7	breast:
8	chr15:75248574..75249256-chr7:2394272..2394802,2	Hela-S3	cervix:
9	chr15:75182085..75184679-chr15:75247604..75250598,2	MCF-7	breast:
10	chr15:75226664..75233309-chr15:75245862..75252227,16	K562	blood:
11	chr15:75248614..75249511-chr5:162887169..162888050,2	Hela-S3	cervix:
12	chr15:75107962..75109830-chr15:75247955..75249471,2	K562	blood:
13	chr15:75246752..75249656-chr15:75313121..75316891,3	K562	blood:
14	chr15:75247632..75249513-chr15:75319371..75321803,2	MCF-7	breast:
15	chr15:75181382..75185367-chr15:75245501..75252189,8	K562	blood:
16	chr15:75074533..75077400-chr15:75247038..75249331,2	MCF-7	breast:
17	chr14:81687022..81687670-chr15:75248682..75249196,2	Hela-S3	cervix:
18	chr15:75197370..75200380-chr15:75247025..75249904,3	MCF-7	breast:
19	chr15:75134593..75136676-chr15:75247766..75251919,4	MCF-7	breast:
20	chr15:75248607..75249544-chr3:183853080..183853960,2	Hela-S3	cervix:
21	chr15:38544473..38545101-chr15:75248720..75249565,2	Hela-S3	cervix:
22	chr15:75197919..75201119-chr15:75247045..75249740,3	K562	blood:
23	chr15:75248174..75249163-chr6:86388387..86389171,2	Hela-S3	cervix:
24	chr14:50234573..50235413-chr15:75248615..75249128,2	Hela-S3	cervix:
25	chr15:75248609..75249523-chr3:128901754..128902749,2	Hela-S3	cervix:
26	chr15:75246342..75249068-chr15:75626976..75630362,3	K562	blood:
27	chr15:75247469..75252493-chr15:75314645..75318771,7	MCF-7	breast:
28	chr15:75117625..75119967-chr15:75247068..75249643,2	K562	blood:

No data

Variant related genes	Relation type
SCAMP5	TF binding region
ENSG00000072571	Chromatin interaction
ENSG00000179335	Chromatin interaction
ENSG00000140365	Chromatin interaction
ENSG00000145191	Chromatin interaction
ENSG00000178741	Chromatin interaction
ENSG00000169714	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000213578	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000138621	Chromatin interaction
ENSG00000260483	Chromatin interaction
ENSG00000166068	Chromatin interaction
ENSG00000198794	Chromatin interaction
ENSG00000165417	Chromatin interaction
ENSG00000165516	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000261606	Chromatin interaction
ENSG00000203875	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000106263	Chromatin interaction
ENSG00000167173	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000167996	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1612	chr15:75247725-75281284	Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75246400-75249000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:75246600-75248800	Flanking Active TSS	Duodenum Mucosa	Duodenum
3	chr15:75246600-75249000	Flanking Active TSS	Colonic Mucosa	Colon
4	chr15:75246800-75248800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
5	chr15:75246800-75251000	Active TSS	Ovary	ovary
6	chr15:75246800-75251800	Flanking Active TSS	HUVEC	blood vessel
7	chr15:75247000-75248800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
8	chr15:75247000-75249600	Bivalent/Poised TSS	Fetal Brain Female	brain
9	chr15:75247200-75249600	Active TSS	Brain Angular Gyrus	brain
10	chr15:75247400-75249000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr15:75247400-75250000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr15:75247400-75251600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr15:75247600-75249600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:75247600-75250400	Active TSS	Hela-S3	cervix
15	chr15:75247600-75251000	Active TSS	Right Atrium	heart
16	chr15:75247600-75252000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr15:75247800-75248800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
18	chr15:75247800-75249000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:75247800-75249600	Flanking Active TSS	GM12878-XiMat	blood
20	chr15:75247800-75249800	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr15:75247800-75251800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr15:75247800-75252400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr15:75248000-75248800	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr15:75248000-75248800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr15:75248000-75248800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr15:75248000-75248800	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr15:75248000-75248800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
28	chr15:75248000-75248800	Flanking Active TSS	Left Ventricle	heart
29	chr15:75248000-75249000	Flanking Active TSS	Pancreas	Pancrea
30	chr15:75248000-75249200	Flanking Active TSS	Right Ventricle	heart
31	chr15:75248000-75249200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
32	chr15:75248000-75249600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:75248000-75249800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:75248000-75250000	Flanking Active TSS	Liver	Liver
35	chr15:75248200-75248800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:75248200-75248800	Flanking Active TSS	Esophagus	oesophagus
37	chr15:75248200-75248800	Flanking Active TSS	Fetal Lung	lung
38	chr15:75248200-75248800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
39	chr15:75248200-75248800	Flanking Active TSS	Lung	lung
40	chr15:75248200-75249000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr15:75248200-75249000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
42	chr15:75248200-75249000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr15:75248200-75249000	Flanking Bivalent TSS/Enh	Thymus	Thymus
44	chr15:75248200-75249200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr15:75248200-75249200	Weak transcription	Fetal Heart	heart
46	chr15:75248200-75249200	Bivalent/Poised TSS	Osteobl	bone
47	chr15:75248200-75249400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:75248200-75249800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:75248200-75249800	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr15:75248200-75252200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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