Variant report

Variant	rs61745329
Chromosome Location	chr3:160472440-160472441
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	MAX	chr3:160472087-160474294	NB4	blood:	n/a	chr3:160473977-160473987
2	RCOR1	chr3:160472263-160472687	K562	blood:	n/a	n/a
3	ZNF143	chr3:160472130-160474625	H1-hESC	embryonic stem cell:	n/a	chr3:160473995-160474013 chr3:160473396-160473414
4	MAZ	chr3:160472134-160474153	K562	blood:	n/a	chr3:160473977-160473987
5	BACH1	chr3:160472357-160472675	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:160472319-160474500	Raji	blood:	n/a	n/a
7	RUNX3	chr3:160472356-160472629	GM12878	blood:	n/a	n/a
8	SIN3AK20	chr3:160472068-160472593	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr3:160472367-160473668	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr3:160472304-160474711	MCF-7	breast:	n/a	n/a
11	REST	chr3:160472000-160472484	Hela-S3	cervix:	n/a	chr3:160472218-160472236
12	E2F6	chr3:160472236-160474395	A549	lung:	n/a	chr3:160472686-160472696 chr3:160473847-160473856 chr3:160473246-160473257
13	E2F6	chr3:160472309-160473031	K562	blood:	n/a	chr3:160472686-160472696
14	REST	chr3:160471892-160475027	H1-neurons	neurons:	n/a	chr3:160474021-160474034 chr3:160474703-160474717 chr3:160473857-160473870 chr3:160472218-160472236
15	MAX	chr3:160472183-160474736	HepG2	liver:	n/a	chr3:160473977-160473987
16	MAX	chr3:160472154-160474640	HepG2	liver:	n/a	chr3:160473977-160473987
17	REST	chr3:160471990-160473570	U87	brain:	n/a	chr3:160472218-160472236
18	MAX	chr3:160472147-160474643	A549	lung:	n/a	chr3:160473977-160473987
19	REST	chr3:160472077-160472492	K562	blood:	n/a	chr3:160472218-160472236
20	POLR2A	chr3:160472372-160473998	MCF-7	breast:	n/a	n/a
21	TCF12	chr3:160472196-160473471	A549	lung:	n/a	n/a
22	REST	chr3:160471757-160473053	PANC-1	pancreas:	n/a	chr3:160472218-160472236
23	MYC	chr3:160472241-160473520	K562	blood:	n/a	n/a
24	SIN3AK20	chr3:160472196-160474179	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr3:160472277-160474847	H1-neurons	neurons:	n/a	n/a
26	POLR2A	chr3:160472282-160474775	H1-neurons	neurons:	n/a	n/a
27	REST	chr3:160472034-160472474	HepG2	liver:	n/a	chr3:160472218-160472236
28	REST	chr3:160471980-160473092	K562	blood:	n/a	chr3:160472218-160472236
29	POLR2A	chr3:160471871-160473961	MCF10A-Er-Src	breast:	n/a	n/a
30	SIN3AK20	chr3:160472125-160472450	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr3:160472354-160474167	NB4	blood:	n/a	n/a
32	REST	chr3:160471986-160473179	H1-hESC	embryonic stem cell:	n/a	chr3:160472218-160472236
33	CTBP2	chr3:160472287-160474781	H1-hESC	embryonic stem cell:	n/a	n/a
34	REST	chr3:160471664-160473436	ECC-1	luminal epithelium:	n/a	chr3:160472218-160472236
35	REST	chr3:160472020-160473081	SK-N-SH	brain:	n/a	chr3:160472218-160472236
36	REST	chr3:160471956-160473513	MCF-7	breast:	n/a	chr3:160472218-160472236
37	REST	chr3:160472037-160472609	Hela-S3	cervix:	n/a	chr3:160472218-160472236
38	REST	chr3:160472094-160472504	H1-neurons	neurons:	n/a	chr3:160472218-160472236
39	E2F6	chr3:160472114-160474844	H1-hESC	embryonic stem cell:	n/a	chr3:160472686-160472696 chr3:160473847-160473856 chr3:160473246-160473257
40	MAX	chr3:160472189-160473469	K562	blood:	n/a	n/a
41	REST	chr3:160472042-160473052	U87	brain:	n/a	chr3:160472218-160472236
42	MAX	chr3:160472156-160474302	ECC-1	luminal epithelium:	n/a	chr3:160473977-160473987
43	REST	chr3:160472058-160472568	U87	brain:	n/a	chr3:160472218-160472236
44	REST	chr3:160471991-160473426	PFSK-1	brain:	n/a	chr3:160472218-160472236
45	POLR2A	chr3:160472180-160474266	PBDE	blood:	n/a	n/a
46	MAX	chr3:160472079-160473466	ECC-1	luminal epithelium:	n/a	n/a
47	SIN3AK20	chr3:160472096-160473474	H1-hESC	embryonic stem cell:	n/a	n/a
48	KAP1	chr3:160472324-160473503	HEK293	kidney:	n/a	n/a
49	MXI1	chr3:160471784-160475614	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr3:160472393-160474726	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160282301..160284425-chr3:160469832..160472498,3	K562	blood:
2	chr3:160281928..160283694-chr3:160472203..160475526,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KPNA4-1	chr3:160471216-160472930	ENSG00000260572.1
2	lnc-KPNA4-1	chr3:160472382-160473995	NONHSAT093002

Variant related genes	Relation type
PPM1L	TF binding region
ENSG00000229320	Chromatin interaction
ENSG00000186432	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs28404654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28434120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28435386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28460514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28461448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28754816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61746351	1.00[AFR][1000 genomes]
rs62272816	0.80[AFR][1000 genomes]
rs6766594	1.00[AMR][1000 genomes]
rs6767097	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6778473	1.00[AMR][1000 genomes]
rs6779470	1.00[AMR][1000 genomes]
rs6791115	1.00[AMR][1000 genomes]
rs6791258	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 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	chr3:160471800-160472600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
2	chr3:160471800-160472600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr3:160471800-160472800	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr3:160471800-160472800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr3:160471800-160472800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:160471800-160472800	Flanking Active TSS	Osteobl	bone
7	chr3:160471800-160473000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:160471800-160473200	Active TSS	Fetal Brain Male	brain
9	chr3:160471800-160473600	Active TSS	HMEC	breast
10	chr3:160471800-160474600	Active TSS	Fetal Intestine Large	intestine
11	chr3:160471800-160475400	Active TSS	Right Atrium	heart
12	chr3:160471800-160476600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr3:160472000-160472600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
14	chr3:160472000-160472600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr3:160472000-160472600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
16	chr3:160472000-160472600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr3:160472000-160472600	Active TSS	Brain Germinal Matrix	brain
18	chr3:160472000-160472600	Flanking Active TSS	Fetal Thymus	thymus
19	chr3:160472000-160472600	Flanking Active TSS	HUVEC	blood vessel
20	chr3:160472000-160472800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:160472000-160472800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr3:160472000-160472800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:160472000-160472800	Flanking Active TSS	GM12878-XiMat	blood
24	chr3:160472000-160473200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr3:160472000-160473400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:160472000-160473600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:160472000-160473800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:160472000-160473800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:160472000-160473800	Active TSS	Colonic Mucosa	Colon
30	chr3:160472000-160474000	Active TSS	H9 Cell Line	embryonic stem cell
31	chr3:160472000-160474000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:160472000-160474000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:160472000-160474000	Active TSS	Stomach Smooth Muscle	stomach
34	chr3:160472000-160474200	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr3:160472000-160474200	Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr3:160472000-160474200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:160472000-160474200	Active TSS	Fetal Muscle Leg	muscle
38	chr3:160472000-160474200	Active TSS	Pancreas	Pancrea
39	chr3:160472000-160474200	Active TSS	Right Ventricle	heart
40	chr3:160472000-160474400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:160472000-160474400	Active TSS	Placenta Amnion	Placenta Amnion
42	chr3:160472000-160474400	Active TSS	NHDF-Ad	bronchial
43	chr3:160472000-160474800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:160472000-160474800	Active TSS	Stomach Mucosa	stomach
45	chr3:160472000-160475000	Active TSS	Aorta	Aorta
46	chr3:160472000-160475000	Active TSS	Ovary	ovary
47	chr3:160472000-160475200	Active TSS	Left Ventricle	heart
48	chr3:160472000-160475400	Active TSS	Brain Substantia Nigra	brain
49	chr3:160472000-160475600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
50	chr3:160472000-160475600	Flanking Active TSS	Primary B cells from cord blood	blood

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