Variant report

Variant	rs6800513
Chromosome Location	chr3:133525178-133525179
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	POLR2A	chr3:133524431-133525304	GM12878	blood:	n/a	n/a
2	MYC	chr3:133524358-133525316	K562	blood:	n/a	chr3:133524452-133524461
3	RAD21	chr3:133524490-133525205	IMR90	lung:	n/a	chr3:133525006-133525020
4	POLR2A	chr3:133524473-133525335	Hela-S3	cervix:	n/a	n/a
5	MAX	chr3:133524165-133525415	HCT-116	colon:	n/a	chr3:133524452-133524461
6	POLR2A	chr3:133524359-133525249	ProgFib	skin:	n/a	n/a
7	ZNF384	chr3:133525143-133525215	K562	blood:	n/a	n/a
8	ZNF143	chr3:133524240-133525278	Hela-S3	cervix:	n/a	chr3:133524539-133524557 chr3:133524539-133524548 chr3:133525193-133525203 chr3:133524546-133524561 chr3:133524541-133524550
9	POLR2A	chr3:133524398-133525346	GM12892	blood:	n/a	n/a
10	ELF1	chr3:133524316-133525382	MCF-7	breast:	n/a	n/a
11	ELF1	chr3:133524360-133525414	MCF-7	breast:	n/a	n/a
12	GTF2F1	chr3:133525100-133525469	Hela-S3	cervix:	n/a	n/a
13	CHD2	chr3:133524328-133525262	H1-hESC	embryonic stem cell:	n/a	chr3:133524625-133524635 chr3:133524878-133524888
14	POLR2A	chr3:133524404-133525305	GM18526	blood:	n/a	n/a
15	CREB1	chr3:133524336-133525316	K562	blood:	n/a	n/a
16	POLR2A	chr3:133524449-133525506	GM19099	blood:	n/a	n/a
17	POLR2A	chr3:133524418-133525284	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr3:133524454-133525335	HepG2	liver:	n/a	n/a
19	CEBPB	chr3:133524264-133525561	Hela-S3	cervix:	n/a	n/a
20	TBP	chr3:133524417-133525202	K562	blood:	n/a	n/a
21	POLR2A	chr3:133524465-133525274	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr3:133524444-133525353	GM18505	blood:	n/a	n/a
23	POLR2A	chr3:133524482-133525257	GM12878	blood:	n/a	n/a
24	SIN3AK20	chr3:133524461-133525360	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr3:133524474-133525280	GM10847	blood:	n/a	n/a
26	TAF1	chr3:133524505-133525278	H1-hESC	embryonic stem cell:	n/a	n/a
27	E2F4	chr3:133524356-133525267	MCF10A-Er-Src	breast:	n/a	chr3:133524631-133524640
28	MAZ	chr3:133525128-133525297	K562	blood:	n/a	n/a
29	MAX	chr3:133524283-133525314	A549	lung:	n/a	chr3:133524452-133524461
30	NRF1	chr3:133525076-133525196	GM12878	blood:	n/a	n/a
31	MXI1	chr3:133524293-133525333	HepG2	liver:	n/a	n/a
32	POLR2A	chr3:133524467-133525283	GM18951	blood:	n/a	n/a
33	ELF1	chr3:133524949-133525231	K562	blood:	n/a	n/a
34	POLR2A	chr3:133524895-133525277	H1-hESC	embryonic stem cell:	n/a	n/a
35	TAF1	chr3:133525047-133525275	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr3:133524399-133525229	MCF-7	breast:	n/a	n/a
37	POLR2A	chr3:133524424-133525393	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr3:133524355-133525449	GM12892	blood:	n/a	n/a
39	MAX	chr3:133524361-133525315	SK-N-SH	brain:	n/a	chr3:133524452-133524461
40	CREB1	chr3:133524365-133525335	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr3:133524897-133525210	GM12891	blood:	n/a	n/a
42	POLR2A	chr3:133524459-133525240	HepG2	liver:	n/a	n/a
43	TAF1	chr3:133524952-133525285	GM12878	blood:	n/a	n/a
44	HA-E2F1	chr3:133524102-133525407	MCF-7	breast:	n/a	chr3:133524631-133524640
45	TAF1	chr3:133524387-133525371	H1-hESC	embryonic stem cell:	n/a	n/a
46	RFX5	chr3:133524335-133525303	Hela-S3	cervix:	n/a	chr3:133524345-133524359
47	ELF1	chr3:133524346-133525220	GM12878	blood:	n/a	n/a
48	TBP	chr3:133524418-133525335	H1-hESC	embryonic stem cell:	n/a	n/a
49	PAX5	chr3:133524553-133525272	GM12891	blood:	n/a	chr3:133525099-133525116 chr3:133525098-133525117 chr3:133525100-133525118
50	PML	chr3:133524304-133525368	GM12878	blood:	n/a	chr3:133524453-133524462

No.	Distal block	Cell Line	Cell type
1	chr3:133380350..133382601-chr3:133523415..133526726,4	K562	blood:
2	chr3:133522634..133526763-chr3:133529104..133532905,8	K562	blood:
3	chr3:133523328..133525267-chr3:133529249..133532239,3	MCF-7	breast:
4	chr3:133524847..133526590-chr3:134204244..134205959,2	MCF-7	breast:
5	chr3:133523642..133526680-chr3:133527233..133530883,4	K562	blood:
6	chr3:133379614..133382648-chr3:133523517..133526970,4	MCF-7	breast:
7	chr3:133378019..133382399-chr3:133522860..133528810,6	K562	blood:
8	chr3:133523551..133526872-chr3:133527016..133531055,8	MCF-7	breast:

Variant related genes	Relation type
SRPRB	TF binding region
ENSG00000242337	Chromatin interaction
ENSG00000182923	Chromatin interaction
ENSG00000129055	Chromatin interaction
ENSG00000144867	Chromatin interaction
ENSG00000163781	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12637730	1.00[YRI][hapmap]
rs16840994	1.00[YRI][hapmap]
rs6764794	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9816354	1.00[YRI][hapmap];0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv4018	chr3:133485867-133530668	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 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	chr3:133523800-133525200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
2	chr3:133523800-133525200	Active TSS	Cortex derived primary cultured neurospheres	brain
3	chr3:133523800-133525600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:133523800-133526000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:133523800-133526800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:133524000-133525200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:133524000-133525200	Active TSS	Brain Substantia Nigra	brain
8	chr3:133524000-133525400	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr3:133524000-133525400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:133524000-133525400	Active TSS	Brain Cingulate Gyrus	brain
11	chr3:133524000-133525400	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr3:133524000-133525400	Active TSS	Rectal Smooth Muscle	rectum
13	chr3:133524000-133525400	Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr3:133524000-133525400	Active TSS	Hela-S3	cervix
15	chr3:133524000-133525600	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr3:133524000-133525600	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr3:133524000-133525800	Active TSS	Colon Smooth Muscle	Colon
18	chr3:133524000-133525800	Active TSS	A549	lung
19	chr3:133524200-133525200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:133524200-133525200	Active TSS	Primary T cells from cord blood	blood
21	chr3:133524200-133525200	Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr3:133524200-133525200	Active TSS	Spleen	Spleen
23	chr3:133524200-133525400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:133524200-133525400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:133524200-133525400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:133524200-133525400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:133524200-133525400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:133524200-133525400	Active TSS	Esophagus	oesophagus
29	chr3:133524200-133525400	Active TSS	Fetal Brain Male	brain
30	chr3:133524200-133525600	Active TSS	H9 Cell Line	embryonic stem cell
31	chr3:133524200-133525600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:133524200-133525600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:133524200-133525600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:133524200-133525600	Active TSS	Aorta	Aorta
35	chr3:133524200-133525600	Active TSS	Brain Hippocampus Middle	brain
36	chr3:133524200-133525600	Active TSS	Colonic Mucosa	Colon
37	chr3:133524200-133525600	Active TSS	Fetal Brain Female	brain
38	chr3:133524200-133525600	Active TSS	Fetal Muscle Trunk	muscle
39	chr3:133524200-133525600	Active TSS	Gastric	stomach
40	chr3:133524200-133525600	Active TSS	Left Ventricle	heart
41	chr3:133524200-133525600	Active TSS	Psoas Muscle	Psoas
42	chr3:133524200-133525600	Active TSS	Right Ventricle	heart
43	chr3:133524200-133525600	Active TSS	Stomach Smooth Muscle	stomach
44	chr3:133524200-133525600	Active TSS	HSMM	muscle
45	chr3:133524200-133525800	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr3:133524200-133525800	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr3:133524200-133525800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:133524200-133525800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:133524200-133525800	Active TSS	Fetal Stomach	stomach
50	chr3:133524200-133526000	Active TSS	Breast Myoepithelial Primary Cells	Breast

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