Variant report

Variant	rs3889818
Chromosome Location	chr2:189156809-189156810
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	REST	chr2:189156774-189157289	ECC-1	luminal epithelium:	n/a	chr2:189156995-189157004
2	BCL3	chr2:189155922-189158712	A549	lung:	n/a	chr2:189157703-189157716 chr2:189157243-189157252 chr2:189158254-189158263 chr2:189157574-189157583 chr2:189157571-189157580
3	POLR2A	chr2:189156217-189158013	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr2:189156312-189156882	MCF-7	breast:	n/a	n/a
5	TAF1	chr2:189156176-189158026	SK-N-SH	brain:	n/a	n/a
6	NRF1	chr2:189156089-189158310	SK-N-SH	brain:	n/a	chr2:189157027-189157036
7	TAF1	chr2:189156130-189158032	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZNF143	chr2:189156640-189156829	Hela-S3	cervix:	n/a	n/a
9	MAX	chr2:189156052-189158000	K562	blood:	n/a	chr2:189157243-189157253 chr2:189157025-189157035
10	POLR2A	chr2:189156318-189157874	HEK293	kidney:	n/a	n/a
11	TAF1	chr2:189156390-189157996	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr2:189156181-189158016	HUVEC	blood vessel:	n/a	n/a
13	TEAD4	chr2:189156284-189158057	SK-N-SH	brain:	n/a	chr2:189157766-189157775
14	MAX	chr2:189155919-189156933	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr2:189156372-189156851	ProgFib	skin:	n/a	n/a
16	POLR2A	chr2:189155967-189158844	PFSK-1	brain:	n/a	n/a
17	MAX	chr2:189155952-189158089	SK-N-SH	brain:	n/a	chr2:189157243-189157253 chr2:189157025-189157035
18	POLR2A	chr2:189155830-189159188	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr2:189155955-189158565	Hela-S3	cervix:	n/a	n/a
20	CCNT2	chr2:189156254-189157761	K562	blood:	n/a	chr2:189157430-189157439
21	E2F6	chr2:189156081-189157829	K562	blood:	n/a	chr2:189157240-189157250 chr2:189156415-189156430 chr2:189157242-189157251
22	TEAD4	chr2:189156216-189156866	K562	blood:	n/a	n/a
23	TAF1	chr2:189156372-189157966	ECC-1	luminal epithelium:	n/a	n/a
24	EP300	chr2:189156203-189158072	SK-N-SH	brain:	n/a	chr2:189157240-189157256
25	MAZ	chr2:189155877-189158053	K562	blood:	n/a	chr2:189157243-189157253 chr2:189157025-189157035
26	RAD21	chr2:189155915-189159055	IMR90	lung:	n/a	chr2:189157053-189157062 chr2:189157634-189157648
27	CHD1	chr2:189156501-189161129	H1-hESC	embryonic stem cell:	n/a	n/a
28	SIN3AK20	chr2:189156476-189156821	H1-hESC	embryonic stem cell:	n/a	n/a
29	BCL3	chr2:189156235-189158090	A549	lung:	n/a	chr2:189157703-189157716 chr2:189157243-189157252 chr2:189157574-189157583 chr2:189157571-189157580
30	RAD21	chr2:189156212-189156968	H1-hESC	embryonic stem cell:	n/a	n/a
31	RAD21	chr2:189155947-189157896	H1-hESC	embryonic stem cell:	n/a	chr2:189157053-189157062 chr2:189157634-189157648
32	REST	chr2:189156741-189157586	ECC-1	luminal epithelium:	n/a	chr2:189156995-189157004
33	POLR2A	chr2:189156014-189158150	PANC-1	pancreas:	n/a	n/a
34	GATA1	chr2:189155942-189156940	K562	blood:	n/a	chr2:189156233-189156240 chr2:189156226-189156247 chr2:189156233-189156240 chr2:189156228-189156244 chr2:189156231-189156241 chr2:189156233-189156240
35	CTCF	chr2:189156760-189156910	HMF	breast:	n/a	n/a
36	EP300	chr2:189156202-189158846	ECC-1	luminal epithelium:	n/a	chr2:189157240-189157256 chr2:189158507-189158521
37	SMC3	chr2:189155238-189159444	SK-N-SH	brain:	n/a	chr2:189157006-189157013
38	HMGN3	chr2:189156243-189157769	K562	blood:	n/a	n/a
39	REST	chr2:189156170-189157853	SK-N-SH	brain:	n/a	chr2:189156995-189157004
40	SIN3AK20	chr2:189156059-189156922	A549	lung:	n/a	n/a
41	SIN3AK20	chr2:189156736-189158063	SK-N-SH	brain:	n/a	n/a
42	SMC3	chr2:189156278-189156893	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr2:189156399-189156888	Hela-S3	cervix:	n/a	n/a
44	ZBTB7A	chr2:189156187-189157789	ECC-1	luminal epithelium:	n/a	chr2:189157504-189157511
45	MYC	chr2:189156734-189157738	MCF-7	breast:	n/a	chr2:189157243-189157253 chr2:189157025-189157035
46	POLR2A	chr2:189155853-189157960	K562	blood:	n/a	n/a
47	TBP	chr2:189155902-189159014	H1-hESC	embryonic stem cell:	n/a	n/a
48	REST	chr2:189156702-189157883	PFSK-1	brain:	n/a	chr2:189156995-189157004
49	CTCF	chr2:189156760-189156910	Hela-S3	cervix:	n/a	n/a
50	TEAD4	chr2:189156033-189158054	ECC-1	luminal epithelium:	n/a	chr2:189157766-189157775

No.	Distal block	Cell Line	Cell type
1	chr2:189140399..189142820-chr2:189154292..189157242,2	MCF-7	breast:
2	chr2:189156064..189158162-chr2:189159992..189162914,5	K562	blood:
3	chr2:189148121..189153367-chr2:189154784..189162424,9	K562	blood:
4	chr2:189150760..189152775-chr2:189155394..189157750,2	MCF-7	breast:
5	chr2:189155055..189158409-chr2:189159948..189163832,8	K562	blood:
6	chr2:189156802..189157479-chr2:189233856..189234710,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL3A1-2	chr2:189156434-189156893	NONHSAT076030

Variant related genes	Relation type
GULP1	TF binding region
LINC01090	TF binding region
ENSG00000231689	Chromatin interaction
ENSG00000207951	Chromatin interaction
ENSG00000200650	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10168305	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10175838	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10179836	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10179899	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10180000	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10180687	0.85[EUR][1000 genomes]
rs10184703	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10187646	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10187791	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10189197	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10189416	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10195059	0.86[ASN][1000 genomes]
rs10199261	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10204144	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10209424	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10210696	0.86[EUR][1000 genomes]
rs10469734	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10469735	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693490	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12693491	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693492	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693493	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693494	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693495	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693497	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12987018	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12987194	0.86[EUR][1000 genomes]
rs12987553	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12995727	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13000379	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13003679	0.93[ASN][1000 genomes]
rs13003972	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13007721	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13021294	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13027220	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13032231	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13382200	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13385282	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13390401	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13390524	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13394232	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13394422	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13403228	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13404958	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13413164	0.93[ASN][1000 genomes]
rs13429075	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2004888	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28572636	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34000922	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34066981	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34135749	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34140900	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34353529	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34358898	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34484855	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34557812	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34575499	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34583514	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34762706	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34762794	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35015018	0.86[ASN][1000 genomes]
rs35060323	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35196443	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35325130	0.86[ASN][1000 genomes]
rs35442646	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35536225	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35877064	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36174757	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4128404	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4261684	0.86[EUR][1000 genomes]
rs4361092	0.86[EUR][1000 genomes]
rs4430902	0.86[EUR][1000 genomes]
rs4458180	0.83[EUR][1000 genomes]
rs4535011	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4640356	0.86[EUR][1000 genomes]
rs4667219	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4667220	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4992742	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4992743	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4992744	0.86[EUR][1000 genomes]
rs55852512	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6434277	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66948063	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66993342	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6718697	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6720002	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6720983	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67240894	0.86[EUR][1000 genomes]
rs67344766	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67389016	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6748077	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67621133	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67804812	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72901602	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72909512	0.86[ASN][1000 genomes]
rs72909520	0.86[ASN][1000 genomes]
rs72911423	0.86[ASN][1000 genomes]
rs7571197	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7571494	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7579554	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7593232	0.86[ASN][1000 genomes]
rs9288152	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9288153	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9808523	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9808557	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1010394	chr2:188994398-189284092	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv998395	chr2:189018246-189284092	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189155200-189161800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:189155400-189158400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:189155400-189160800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:189155400-189161000	Active TSS	Aorta	Aorta
5	chr2:189155400-189161200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:189155400-189161200	Active TSS	K562	blood
7	chr2:189155400-189161600	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr2:189155600-189157000	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr2:189155600-189157200	Active TSS	Brain Germinal Matrix	brain
10	chr2:189155600-189158600	Active TSS	Fetal Brain Female	brain
11	chr2:189155600-189158600	Active TSS	NHLF	lung
12	chr2:189155600-189161200	Active TSS	H9 Cell Line	embryonic stem cell
13	chr2:189155600-189161600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:189155600-189161800	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr2:189155800-189157800	Active TSS	Brain Hippocampus Middle	brain
16	chr2:189155800-189157800	Active TSS	Osteobl	bone
17	chr2:189155800-189158000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:189155800-189158000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:189155800-189158200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr2:189155800-189158200	Active TSS	HMEC	breast
21	chr2:189155800-189158400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:189155800-189158400	Active TSS	Placenta Amnion	Placenta Amnion
23	chr2:189155800-189158800	Active TSS	Brain Anterior Caudate	brain
24	chr2:189155800-189159000	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr2:189155800-189159200	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr2:189155800-189159200	Active TSS	Ovary	ovary
27	chr2:189155800-189159200	Active TSS	Psoas Muscle	Psoas
28	chr2:189155800-189159400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:189155800-189159400	Active TSS	Fetal Intestine Small	intestine
30	chr2:189155800-189159400	Active TSS	Right Atrium	heart
31	chr2:189155800-189159800	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr2:189155800-189160000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:189155800-189160200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr2:189155800-189160200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr2:189155800-189160200	Active TSS	Fetal Intestine Large	intestine
36	chr2:189155800-189161200	Active TSS	Placenta	Placenta
37	chr2:189155800-189161200	Active TSS	A549	lung
38	chr2:189155800-189161400	Active TSS	H1 Cell Line	embryonic stem cell
39	chr2:189156000-189157400	Active TSS	Pancreas	Pancrea
40	chr2:189156000-189157400	Active TSS	Small Intestine	intestine
41	chr2:189156000-189157400	Active TSS	Hela-S3	cervix
42	chr2:189156000-189157600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:189156000-189157600	Flanking Active TSS	Liver	Liver
44	chr2:189156000-189157800	Active TSS	Brain Cingulate Gyrus	brain
45	chr2:189156000-189157800	Active TSS	Brain Substantia Nigra	brain
46	chr2:189156000-189157800	Active TSS	Left Ventricle	heart
47	chr2:189156000-189157800	Active TSS	HSMMtube	muscle
48	chr2:189156000-189158000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:189156000-189158000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:189156000-189158000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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