Variant report

Variant	rs2028899
Chromosome Location	chr2:85767969-85767970
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:91)
CpG islands
(count:0)
Chromatin interactive
region (count:44)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:91 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:85764818-85775931	U87	brain:	n/a	n/a
2	POLR2A	chr2:85764716-85770554	GM12878	blood:	n/a	n/a
3	SIX5	chr2:85764471-85768062	A549	lung:	n/a	n/a
4	MXI1	chr2:85765848-85768858	K562	blood:	n/a	chr2:85766928-85766937
5	BCLAF1	chr2:85765506-85768054	K562	blood:	n/a	chr2:85767948-85767957 chr2:85766915-85766928 chr2:85766117-85766130 chr2:85765969-85765982 chr2:85767338-85767347
6	POLR2A	chr2:85764187-85776473	PBDE	blood:	n/a	n/a
7	POLR2A	chr2:85764748-85775047	K562	blood:	n/a	n/a
8	POLR2A	chr2:85764404-85775965	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:85764649-85768074	GM12892	blood:	n/a	n/a
10	POLR2A	chr2:85764666-85767973	HUVEC	blood vessel:	n/a	n/a
11	MYBL2	chr2:85764639-85768149	HepG2	liver:	n/a	n/a
12	NFATC1	chr2:85765547-85768564	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:85764617-85775797	GM12892	blood:	n/a	n/a
14	POLR2A	chr2:85764340-85770626	GM12891	blood:	n/a	n/a
15	POLR2A	chr2:85767954-85767978	MCF-7	breast:	n/a	n/a
16	POLR2A	chr2:85764661-85767972	K562	blood:	n/a	n/a
17	POLR2A	chr2:85764737-85768102	HL-60	blood:	n/a	n/a
18	POLR2A	chr2:85764639-85770654	SK-N-SH	brain:	n/a	n/a
19	MAFF	chr2:85766958-85768235	K562	blood:	n/a	n/a
20	BCL3	chr2:85764487-85768038	A549	lung:	n/a	chr2:85767948-85767957 chr2:85766915-85766928 chr2:85766117-85766130 chr2:85765161-85765170 chr2:85765969-85765982 chr2:85767338-85767347
21	MBD4	chr2:85764705-85768206	HepG2	liver:	n/a	n/a
22	POLR2A	chr2:85767820-85767971	H1-hESC	embryonic stem cell:	n/a	n/a
23	ATF3	chr2:85765537-85768775	A549	lung:	n/a	chr2:85766904-85766913
24	SREBP1	chr2:85763798-85768460	GM12878	blood:	n/a	n/a
25	CHD1	chr2:85764795-85768197	H1-hESC	embryonic stem cell:	n/a	chr2:85766159-85766169
26	POLR2A	chr2:85764697-85770730	HCT-116	colon:	n/a	n/a
27	HEY1	chr2:85764668-85775178	K562	blood:	n/a	chr2:85766901-85766916
28	POLR2A	chr2:85764195-85777893	PANC-1	pancreas:	n/a	n/a
29	ARID3A	chr2:85765599-85768400	K562	blood:	n/a	n/a
30	GATA3	chr2:85764646-85770027	A549	lung:	n/a	n/a
31	CTCF	chr2:85763722-85768035	A549	lung:	n/a	n/a
32	CEBPB	chr2:85766833-85767987	K562	blood:	n/a	chr2:85767472-85767483
33	SIN3A	chr2:85764817-85768086	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr2:85764638-85775973	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr2:85764640-85768009	GM12891	blood:	n/a	n/a
36	POLR2A	chr2:85764425-85776507	U87	brain:	n/a	n/a
37	POLR2A	chr2:85764254-85778359	SK-N-MC	brain:	n/a	n/a
38	RCOR1	chr2:85765680-85767999	K562	blood:	n/a	n/a
39	RFX5	chr2:85766745-85768688	K562	blood:	n/a	chr2:85767754-85767771
40	HEY1	chr2:85764647-85768527	HepG2	liver:	n/a	chr2:85766901-85766916
41	MYC	chr2:85764917-85767971	K562	blood:	n/a	chr2:85765885-85765895 chr2:85766929-85766939 chr2:85766931-85766947 chr2:85766928-85766939 chr2:85766930-85766939 chr2:85766029-85766038 chr2:85766928-85766939 chr2:85766931-85766938 chr2:85766927-85766940 chr2:85766929-85766938 chr2:85765458-85765467 chr2:85766927-85766940 chr2:85766928-85766937 chr2:85766929-85766939 chr2:85766928-85766939 chr2:85766665-85766674 chr2:85766928-85766938
42	TEAD4	chr2:85765526-85768047	HepG2	liver:	n/a	n/a
43	POLR2A	chr2:85764329-85770781	Hela-S3	cervix:	n/a	n/a
44	MXI1	chr2:85764724-85767993	IMR90	lung:	n/a	chr2:85766928-85766937
45	EP300	chr2:85767123-85768128	GM12878	blood:	n/a	n/a
46	POLR2A	chr2:85764641-85768514	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr2:85764678-85768088	GM12892	blood:	n/a	n/a
48	MXI1	chr2:85763373-85768685	SK-N-SH	brain:	n/a	chr2:85766928-85766937
49	POLR2A	chr2:85764698-85770601	GM12878	blood:	n/a	n/a
50	POLR2A	chr2:85764661-85768042	GM12891	blood:	n/a	n/a

No data

(count:44 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85594968..85598599-chr2:85764725..85768388,5	K562	blood:
2	chr2:85551217..85557082-chr2:85763566..85768403,18	K562	blood:
3	chr2:85579454..85586122-chr2:85763967..85769855,18	K562	blood:
4	chr2:85644216..85654950-chr2:85758513..85769717,70	MCF-7	breast:
5	chr2:85764946..85769175-chr2:85814893..85818821,4	K562	blood:
6	chr2:85764595..85768669-chr2:85824476..85831716,9	MCF-7	breast:
7	chr2:85765231..85769518-chr2:85784806..85790228,6	MCF-7	breast:
8	chr2:85764842..85767974-chr2:85803132..85805827,5	MCF-7	breast:
9	chr2:85765237..85769549-chr2:85821409..85826975,10	K562	blood:
10	chr2:85579256..85583791-chr2:85762380..85768080,8	MCF-7	breast:
11	chr2:85639277..85641952-chr2:85764715..85768056,5	MCF-7	breast:
12	chr2:85764353..85768297-chr2:85801597..85805697,4	K562	blood:
13	chr2:85549396..85557177-chr2:85763484..85769653,16	MCF-7	breast:
14	chr2:85616263..85635094-chr2:85763849..85770697,56	MCF-7	breast:
15	chr2:85568802..85571151-chr2:85767821..85769342,2	K562	blood:
16	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
17	chr2:85764018..85768553-chr2:85822883..85829718,12	MCF-7	breast:
18	chr2:85627997..85630294-chr2:85764975..85768258,3	K562	blood:
19	chr2:38977031..38979396-chr2:85765814..85768332,2	K562	blood:
20	chr2:85765001..85768151-chr2:85794146..85798905,4	K562	blood:
21	chr2:85764765..85769369-chr2:85840508..85847982,10	K562	blood:
22	chr2:85553933..85556684-chr2:85766615..85769181,3	MCF-7	breast:
23	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
24	chr2:85765167..85768270-chr2:85828920..85831672,3	K562	blood:
25	chr2:85611082..85627761-chr2:85764356..85782623,83	K562	blood:
26	chr2:85572304..85574564-chr2:85765352..85768269,2	MCF-7	breast:
27	chr2:85764082..85769632-chr2:85809376..85814783,9	K562	blood:
28	chr2:74685306..74687081-chr2:85766606..85768350,2	K562	blood:
29	chr1:46152933..46153874-chr2:85767773..85768336,2	NB4	blood:
30	chr2:85579726..85583616-chr2:85764675..85769618,5	MCF-7	breast:
31	chr2:85764346..85769986-chr2:85836202..85840842,10	MCF-7	breast:
32	chr2:85767293..85770194-chr2:85815993..85818775,2	MCF-7	breast:
33	chr2:85658029..85667242-chr2:85763719..85770665,19	MCF-7	breast:
34	chr2:85764454..85770994-chr2:85819148..85831427,14	K562	blood:
35	chr2:85551607..85557241-chr2:85763492..85768403,12	K562	blood:
36	chr2:85642633..85666582-chr2:85757429..85771032,137	MCF-7	breast:
37	chr2:85635858..85639239-chr2:85765093..85768517,6	MCF-7	breast:
38	chr2:85196390..85199839-chr2:85765412..85768787,4	MCF-7	breast:
39	chr2:85764767..85768368-chr2:85809376..85813309,5	K562	blood:
40	chr2:85617430..85626766-chr2:85763113..85771250,22	MCF-7	breast:
41	chr2:85580032..85585466-chr2:85764930..85768997,13	K562	blood:
42	chr2:85766117..85770203-chr2:85837145..85839440,4	K562	blood:
43	chr2:85764476..85768967-chr2:85811222..85814196,4	MCF-7	breast:
44	chr2:85766264..85769158-chr5:107716614..107718992,2	MCF-7	breast:

No data

Variant related genes	Relation type
MAT2A	TF binding region
ENSG00000199936	Chromatin interaction
ENSG00000042445	Chromatin interaction
ENSG00000159596	Chromatin interaction
ENSG00000152291	Chromatin interaction
ENSG00000244399	Chromatin interaction
ENSG00000266536	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000252293	Chromatin interaction
ENSG00000168899	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000273196	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000239779	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000168890	Chromatin interaction
ENSG00000207207	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000176407	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000145743	Chromatin interaction
ENSG00000270532	Chromatin interaction
ENSG00000168887	Chromatin interaction
ENSG00000242095	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12463705	0.83[EUR][1000 genomes]
rs12468473	0.83[EUR][1000 genomes]
rs12470070	0.83[EUR][1000 genomes]
rs12470640	0.83[EUR][1000 genomes]
rs12471036	0.83[EUR][1000 genomes]
rs12473382	0.83[EUR][1000 genomes]
rs17026447	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17792131	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2028106	1.00[AMR][1000 genomes]
rs6704863	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6707308	0.86[EUR][1000 genomes]
rs68055751	0.83[EUR][1000 genomes]
rs72843835	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72843836	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72843839	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72843846	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72843854	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs72843867	0.82[EUR][1000 genomes]
rs72844407	0.83[EUR][1000 genomes]
rs72844409	0.83[EUR][1000 genomes]
rs72844415	0.83[EUR][1000 genomes]
rs72844416	0.83[EUR][1000 genomes]
rs72844417	0.83[EUR][1000 genomes]
rs72844418	0.83[EUR][1000 genomes]
rs72844421	0.83[EUR][1000 genomes]
rs72844426	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72844445	1.00[AMR][1000 genomes];0.89[EUR][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	nsv1005351	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv535803	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription 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	198 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	chr2:85764200-85768600	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr2:85764600-85768200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:85764600-85768200	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr2:85764600-85768200	Active TSS	Brain Angular Gyrus	brain
5	chr2:85764600-85768200	Active TSS	Fetal Stomach	stomach
6	chr2:85764600-85768600	Active TSS	Aorta	Aorta
7	chr2:85764800-85768000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:85764800-85768000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:85764800-85768000	Active TSS	Sigmoid Colon	Sigmoid Colon
10	chr2:85764800-85768200	Active TSS	Lung	lung
11	chr2:85764800-85768400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:85764800-85768400	Active TSS	Ovary	ovary
13	chr2:85764800-85768600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr2:85764800-85768600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:85764800-85768600	Active TSS	Pancreas	Pancrea
16	chr2:85764800-85769200	Active TSS	Right Ventricle	heart
17	chr2:85765000-85768000	Active TSS	Brain Cingulate Gyrus	brain
18	chr2:85765000-85768000	Active TSS	Esophagus	oesophagus
19	chr2:85765000-85768000	Active TSS	Gastric	stomach
20	chr2:85765000-85768000	Active TSS	Small Intestine	intestine
21	chr2:85765000-85768200	Active TSS	Fetal Intestine Large	intestine
22	chr2:85765000-85768200	Active TSS	Fetal Intestine Small	intestine
23	chr2:85765000-85768200	Active TSS	HSMMtube	muscle
24	chr2:85765000-85768400	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr2:85765000-85768600	Active TSS	Stomach Mucosa	stomach
26	chr2:85765200-85768400	Active TSS	Colonic Mucosa	Colon
27	chr2:85765200-85768400	Active TSS	Rectal Smooth Muscle	rectum
28	chr2:85765200-85768600	Active TSS	Left Ventricle	heart
29	chr2:85765200-85768800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:85765200-85769000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:85765200-85769400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:85765400-85768200	Active TSS	Brain Germinal Matrix	brain
33	chr2:85765400-85768200	Active TSS	Fetal Brain Female	brain
34	chr2:85765400-85768200	Active TSS	Fetal Heart	heart
35	chr2:85765400-85768400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:85765600-85768200	Active TSS	Fetal Brain Male	brain
37	chr2:85765600-85768400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:85766400-85770200	Transcr. at gene 5' and 3'	Dnd41	blood
39	chr2:85766400-85770600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
40	chr2:85766400-85770600	Transcr. at gene 5' and 3'	NHLF	lung
41	chr2:85766600-85770800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:85766800-85768200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:85766800-85769000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:85766800-85770000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:85766800-85770200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
46	chr2:85766800-85770600	Transcr. at gene 5' and 3'	A549	lung
47	chr2:85767000-85768000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr2:85767000-85768000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr2:85767000-85768000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr2:85767000-85768000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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