Variant report

Variant	rs58689622
Chromosome Location	chr3:155462214-155462215
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	chr3:155461985-155462260	ProgFib	skin:	n/a	n/a
2	CTBP2	chr3:155461816-155463206	H1-hESC	embryonic stem cell:	n/a	n/a
3	SP1	chr3:155461843-155463352	A549	lung:	n/a	chr3:155462884-155462895 chr3:155462885-155462899
4	POLR2A	chr3:155461795-155462288	HCT-116	colon:	n/a	n/a
5	ELF1	chr3:155462106-155463176	MCF-7	breast:	n/a	chr3:155462832-155462841
6	MXI1	chr3:155461828-155462321	H1-hESC	embryonic stem cell:	n/a	chr3:155461984-155461999 chr3:155461986-155462001
7	ZBTB7A	chr3:155462161-155462350	HepG2	liver:	n/a	n/a
8	HMGN3	chr3:155461912-155463020	K562	blood:	n/a	n/a
9	POLR2A	chr3:155461711-155463117	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr3:155461971-155462437	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:155461782-155463169	H1-hESC	embryonic stem cell:	n/a	n/a
12	SIN3A	chr3:155461524-155463101	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:155461905-155462379	HepG2	liver:	n/a	n/a
14	BACH1	chr3:155462057-155463080	H1-hESC	embryonic stem cell:	n/a	n/a
15	REST	chr3:155461875-155462384	A549	lung:	n/a	chr3:155462231-155462244 chr3:155462011-155462024
16	POLR2A	chr3:155461879-155462299	A549	lung:	n/a	n/a
17	POLR2A	chr3:155461880-155463078	MCF-7	breast:	n/a	n/a
18	JUND	chr3:155462079-155462284	K562	blood:	n/a	n/a
19	TAF1	chr3:155461838-155463036	H1-neurons	neurons:	n/a	n/a
20	RCOR1	chr3:155461843-155462373	K562	blood:	n/a	n/a
21	CREB1	chr3:155462159-155463115	HepG2	liver:	n/a	n/a
22	HA-E2F1	chr3:155461710-155463204	MCF-7	breast:	n/a	chr3:155462003-155462012 chr3:155462857-155462866
23	MAX	chr3:155461795-155462571	A549	lung:	n/a	chr3:155461990-155461999
24	HEY1	chr3:155461817-155462265	HepG2	liver:	n/a	chr3:155462017-155462032
25	POLR2A	chr3:155461880-155462221	A549	lung:	n/a	n/a
26	YY1	chr3:155461923-155462443	A549	lung:	n/a	n/a
27	REST	chr3:155461339-155463168	H1-neurons	neurons:	n/a	chr3:155462231-155462244 chr3:155462011-155462024
28	MAX	chr3:155461818-155463098	ECC-1	luminal epithelium:	n/a	chr3:155461990-155461999 chr3:155462885-155462895
29	NFYB	chr3:155462147-155462345	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:155461857-155463020	Raji	blood:	n/a	n/a
31	MYC	chr3:155461949-155463142	K562	blood:	n/a	chr3:155461990-155461999 chr3:155462885-155462895
32	POLR2A	chr3:155461908-155462230	H1-hESC	embryonic stem cell:	n/a	n/a
33	MAX	chr3:155461801-155463231	MCF-7	breast:	n/a	chr3:155461990-155461999 chr3:155462885-155462895
34	SIN3AK20	chr3:155461741-155463079	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr3:155461966-155462214	HepG2	liver:	n/a	n/a
36	YY1	chr3:155461970-155462239	HCT-116	colon:	n/a	n/a
37	POLR2A	chr3:155461874-155463135	HL-60	blood:	n/a	n/a
38	RCOR1	chr3:155462085-155462289	HepG2	liver:	n/a	n/a
39	POLR2A	chr3:155461852-155462616	HepG2	liver:	n/a	n/a
40	SPI1	chr3:155462015-155463180	HL-60	blood:	n/a	n/a
41	UBTF	chr3:155462038-155463004	K562	blood:	n/a	n/a
42	MXI1	chr3:155461328-155463302	SK-N-SH	brain:	n/a	chr3:155461984-155461999 chr3:155461986-155462001
43	POLR2A	chr3:155461883-155462275	HepG2	liver:	n/a	n/a
44	POLR2A	chr3:155461853-155462256	HCT-116	colon:	n/a	n/a
45	NRF1	chr3:155461510-155462973	SK-N-SH	brain:	n/a	chr3:155462002-155462016 chr3:155461999-155462013 chr3:155462001-155462012 chr3:155462002-155462011 chr3:155462002-155462013
46	MAX	chr3:155461844-155463173	K562	blood:	n/a	chr3:155461990-155461999 chr3:155462885-155462895
47	SPI1	chr3:155462104-155462903	GM12878	blood:	n/a	n/a
48	POLR2A	chr3:155461905-155462221	K562	blood:	n/a	n/a
49	MAZ	chr3:155461945-155463123	K562	blood:	n/a	chr3:155461990-155461999 chr3:155462885-155462895
50	REST	chr3:155461826-155462601	H1-neurons	neurons:	n/a	chr3:155462231-155462244 chr3:155462011-155462024

No.	Distal block	Cell Line	Cell type
1	chr3:155461486..155463918-chr3:155586998..155589713,4	K562	blood:
2	chr3:155461195..155464539-chr3:155588373..155590107,3	MCF-7	breast:
3	chr3:155460891..155464537-chr3:155570941..155574143,3	MCF-7	breast:
4	chr3:155462054..155464221-chr3:155571081..155573574,2	MCF-7	breast:
5	chr3:155461486..155465793-chr3:155586998..155592801,6	K562	blood:
6	chr3:155461523..155464397-chr3:155587900..155591398,5	MCF-7	breast:
7	chr3:155461931..155462531-chr8:43096224..43096734,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214919	TF binding region
ENSG00000169359	Chromatin interaction
ENSG00000163655	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs4680213	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58881566	1.00[AMR][1000 genomes]
rs6789127	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6802192	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7638454	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[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	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers 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	11 gene(s)	inside rSNPs	diseases
2	nsv829763	chr3:155417552-155470079	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58689622	TRAP1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155460800-155463600	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr3:155461000-155464400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:155461200-155462800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
4	chr3:155461200-155463000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:155461200-155464200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:155461400-155462600	Active TSS	Fetal Kidney	kidney
7	chr3:155461400-155462800	Flanking Bivalent TSS/Enh	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:155461400-155462800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:155461400-155462800	Active TSS	Fetal Brain Male	brain
10	chr3:155461400-155462800	Active TSS	Hela-S3	cervix
11	chr3:155461400-155463000	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr3:155461400-155463000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:155461400-155463000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:155461400-155463000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
15	chr3:155461400-155463000	Active TSS	Sigmoid Colon	Sigmoid Colon
16	chr3:155461400-155463000	Flanking Bivalent TSS/Enh	Dnd41	blood
17	chr3:155461400-155463200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
18	chr3:155461400-155463200	Active TSS	Left Ventricle	heart
19	chr3:155461400-155463200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
20	chr3:155461400-155463200	Bivalent/Poised TSS	HSMM	muscle
21	chr3:155461400-155463400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:155461400-155463400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
23	chr3:155461400-155463600	Active TSS	Pancreas	Pancrea
24	chr3:155461400-155463800	Active TSS	Gastric	stomach
25	chr3:155461400-155463800	Active TSS	Right Ventricle	heart
26	chr3:155461400-155463800	Active TSS	A549	lung
27	chr3:155461400-155463800	Active TSS	NHLF	lung
28	chr3:155461400-155464000	Active TSS	H9 Cell Line	embryonic stem cell
29	chr3:155461400-155464000	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr3:155461400-155464000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:155461400-155464000	Active TSS	Right Atrium	heart
32	chr3:155461400-155464200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr3:155461400-155464200	Active TSS	Brain Angular Gyrus	brain
34	chr3:155461400-155464200	Active TSS	Brain Cingulate Gyrus	brain
35	chr3:155461600-155462400	Bivalent/Poised TSS	Fetal Brain Female	brain
36	chr3:155461600-155462400	Bivalent/Poised TSS	Stomach Mucosa	stomach
37	chr3:155461600-155462800	Active TSS	Stomach Smooth Muscle	stomach
38	chr3:155461600-155463000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:155461600-155463000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:155461600-155463000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:155461600-155463000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:155461600-155463000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:155461600-155463000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
44	chr3:155461600-155463000	Flanking Active TSS	Liver	Liver
45	chr3:155461600-155463000	Bivalent/Poised TSS	HSMMtube	muscle
46	chr3:155461600-155463000	Bivalent/Poised TSS	NHDF-Ad	bronchial
47	chr3:155461600-155463200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
48	chr3:155461600-155463200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr3:155461600-155463200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
50	chr3:155461600-155463200	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood

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