Variant report

Variant	rs61746351
Chromosome Location	chr3:160472819-160472820
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	chr3:160472503-160474219	SK-N-MC	brain:	n/a	n/a
2	MAX	chr3:160472087-160474294	NB4	blood:	n/a	chr3:160473977-160473987
3	ELF1	chr3:160472640-160473363	MCF-7	breast:	n/a	chr3:160473211-160473223
4	POLR2A	chr3:160472766-160472952	HepG2	liver:	n/a	n/a
5	BRCA1	chr3:160472637-160473174	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:160472536-160473645	HUVEC	blood vessel:	n/a	n/a
7	REST	chr3:160472705-160473256	Hela-S3	cervix:	n/a	n/a
8	ZNF143	chr3:160472130-160474625	H1-hESC	embryonic stem cell:	n/a	chr3:160473995-160474013 chr3:160473396-160473414
9	MAZ	chr3:160472134-160474153	K562	blood:	n/a	chr3:160473977-160473987
10	TEAD4	chr3:160472736-160473330	K562	blood:	n/a	n/a
11	POLR2A	chr3:160472683-160473372	IMR90	lung:	n/a	n/a
12	POLR2A	chr3:160472319-160474500	Raji	blood:	n/a	n/a
13	TAF1	chr3:160472712-160473004	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr3:160472605-160473626	HUVEC	blood vessel:	n/a	n/a
15	HCFC1	chr3:160472473-160473397	K562	blood:	n/a	n/a
16	GATA3	chr3:160472608-160473529	A549	lung:	n/a	chr3:160473157-160473168
17	POLR2A	chr3:160472538-160474622	HL-60	blood:	n/a	n/a
18	POLR2A	chr3:160472615-160473692	Gliobla	brain:	n/a	n/a
19	POLR2A	chr3:160472367-160473668	PANC-1	pancreas:	n/a	n/a
20	BHLHE40	chr3:160472794-160473592	HepG2	liver:	n/a	chr3:160473207-160473223 chr3:160473206-160473222
21	TAF1	chr3:160472752-160473046	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:160472466-160473920	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr3:160472591-160473434	GM12892	blood:	n/a	n/a
24	SP1	chr3:160472523-160473802	HCT-116	colon:	n/a	chr3:160472838-160472847
25	PBX3	chr3:160472698-160473481	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr3:160472304-160474711	MCF-7	breast:	n/a	n/a
27	CHD2	chr3:160472558-160473506	HepG2	liver:	n/a	n/a
28	REST	chr3:160472683-160473290	A549	lung:	n/a	n/a
29	STAT5A	chr3:160472739-160473122	K562	blood:	n/a	chr3:160473052-160473061 chr3:160473050-160473064 chr3:160473053-160473062
30	JUND	chr3:160472700-160473481	K562	blood:	n/a	n/a
31	SRF	chr3:160472815-160472964	GM12878	blood:	n/a	n/a
32	MAX	chr3:160472696-160474137	Hela-S3	cervix:	n/a	chr3:160473977-160473987
33	E2F6	chr3:160472236-160474395	A549	lung:	n/a	chr3:160472686-160472696 chr3:160473847-160473856 chr3:160473246-160473257
34	E2F6	chr3:160472309-160473031	K562	blood:	n/a	chr3:160472686-160472696
35	PML	chr3:160472632-160473635	GM12878	blood:	n/a	n/a
36	MAX	chr3:160472713-160473511	SK-N-SH	brain:	n/a	n/a
37	BRCA1	chr3:160472529-160473009	HepG2	liver:	n/a	n/a
38	REST	chr3:160471892-160475027	H1-neurons	neurons:	n/a	chr3:160474021-160474034 chr3:160474703-160474717 chr3:160473857-160473870 chr3:160472218-160472236
39	GABPA	chr3:160472793-160473384	K562	blood:	n/a	n/a
40	MAX	chr3:160472183-160474736	HepG2	liver:	n/a	chr3:160473977-160473987
41	TBP	chr3:160472741-160474080	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAX	chr3:160472803-160473400	K562	blood:	n/a	n/a
43	MAX	chr3:160472154-160474640	HepG2	liver:	n/a	chr3:160473977-160473987
44	POLR2A	chr3:160472756-160472970	HepG2	liver:	n/a	n/a
45	MAX	chr3:160472695-160474798	H1-hESC	embryonic stem cell:	n/a	chr3:160473977-160473987
46	YY1	chr3:160472778-160473029	K562	blood:	n/a	n/a
47	POLR2A	chr3:160472690-160473625	PFSK-1	brain:	n/a	n/a
48	REST	chr3:160471990-160473570	U87	brain:	n/a	chr3:160472218-160472236
49	POLR2A	chr3:160472708-160473525	A549	lung:	n/a	n/a
50	ELF1	chr3:160472814-160473267	A549	lung:	n/a	chr3:160473211-160473223

No.	Distal block	Cell Line	Cell type
1	chr3:160472518..160475131-chr3:161089184..161091851,3	MCF-7	breast:
2	chr3:160472482..160474998-chr3:160940275..160941880,2	MCF-7	breast:
3	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
ENSG00000196542	Chromatin interaction
ENSG00000186432	Chromatin interaction
ENSG00000229320	Chromatin interaction
ENSG00000271052	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs28404654	1.00[AFR][1000 genomes]
rs28434120	1.00[AFR][1000 genomes]
rs28435386	1.00[AFR][1000 genomes]
rs28460514	1.00[AFR][1000 genomes]
rs28461448	1.00[AFR][1000 genomes]
rs28754816	1.00[AFR][1000 genomes]
rs61745329	1.00[AFR][1000 genomes]
rs62272816	0.80[AFR][1000 genomes]
rs6767097	0.94[AFR][1000 genomes]
rs6791258	0.94[AFR][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	chr3:160471800-160473000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr3:160471800-160473200	Active TSS	Fetal Brain Male	brain
3	chr3:160471800-160473600	Active TSS	HMEC	breast
4	chr3:160471800-160474600	Active TSS	Fetal Intestine Large	intestine
5	chr3:160471800-160475400	Active TSS	Right Atrium	heart
6	chr3:160471800-160476600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr3:160472000-160473200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr3:160472000-160473400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:160472000-160473600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:160472000-160473800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:160472000-160473800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:160472000-160473800	Active TSS	Colonic Mucosa	Colon
13	chr3:160472000-160474000	Active TSS	H9 Cell Line	embryonic stem cell
14	chr3:160472000-160474000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:160472000-160474000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:160472000-160474000	Active TSS	Stomach Smooth Muscle	stomach
17	chr3:160472000-160474200	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr3:160472000-160474200	Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr3:160472000-160474200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:160472000-160474200	Active TSS	Fetal Muscle Leg	muscle
21	chr3:160472000-160474200	Active TSS	Pancreas	Pancrea
22	chr3:160472000-160474200	Active TSS	Right Ventricle	heart
23	chr3:160472000-160474400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:160472000-160474400	Active TSS	Placenta Amnion	Placenta Amnion
25	chr3:160472000-160474400	Active TSS	NHDF-Ad	bronchial
26	chr3:160472000-160474800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:160472000-160474800	Active TSS	Stomach Mucosa	stomach
28	chr3:160472000-160475000	Active TSS	Aorta	Aorta
29	chr3:160472000-160475000	Active TSS	Ovary	ovary
30	chr3:160472000-160475200	Active TSS	Left Ventricle	heart
31	chr3:160472000-160475400	Active TSS	Brain Substantia Nigra	brain
32	chr3:160472000-160475600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr3:160472000-160475600	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr3:160472000-160475600	Active TSS	Gastric	stomach
35	chr3:160472000-160476200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
36	chr3:160472000-160476200	Active TSS	Psoas Muscle	Psoas
37	chr3:160472000-160477800	Active TSS	Brain Angular Gyrus	brain
38	chr3:160472000-160477800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:160472200-160473200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:160472200-160473600	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr3:160472200-160474000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:160472200-160474000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:160472200-160474000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:160472200-160474000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:160472200-160474000	Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr3:160472200-160474000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:160472200-160474000	Active TSS	Duodenum Mucosa	Duodenum
48	chr3:160472200-160474000	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr3:160472200-160474000	Active TSS	K562	blood
50	chr3:160472200-160474000	Active TSS	NHEK	skin

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