Variant report

Variant	rs2285143
Chromosome Location	chr1:172502340-172502341
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	RFX5	chr1:172501202-172502449	HepG2	liver:	n/a	chr1:172501603-172501612
2	POLR2A	chr1:172501323-172502928	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:172501058-172503467	Hela-S3	cervix:	n/a	n/a
4	PML	chr1:172501150-172502826	K562	blood:	n/a	n/a
5	MYBL2	chr1:172501329-172502621	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:172500531-172503100	K562	blood:	n/a	n/a
7	POLR2A	chr1:172501130-172503044	PFSK-1	brain:	n/a	n/a
8	MAX	chr1:172501152-172502830	MCF-7	breast:	n/a	n/a
9	CHD2	chr1:172501176-172502803	K562	blood:	n/a	chr1:172502276-172502286
10	TEAD4	chr1:172500605-172503401	K562	blood:	n/a	n/a
11	POLR2A	chr1:172500513-172503382	K562	blood:	n/a	n/a
12	NFYB	chr1:172501309-172502415	Hela-S3	cervix:	n/a	chr1:172501639-172501654 chr1:172502204-172502219 chr1:172501602-172501612 chr1:172501602-172501612 chr1:172502204-172502219
13	RAD21	chr1:172501860-172502378	SK-N-SH_RA	brain:	n/a	chr1:172502268-172502282
14	E2F6	chr1:172501841-172502423	K562	blood:	n/a	chr1:172502135-172502145 chr1:172502199-172502208 chr1:172502028-172502037 chr1:172502208-172502217 chr1:172502275-172502284
15	TAF1	chr1:172502166-172502551	GM12892	blood:	n/a	n/a
16	TCF3	chr1:172501943-172502589	GM12878	blood:	n/a	n/a
17	TAF7	chr1:172502124-172502760	H1-hESC	embryonic stem cell:	n/a	n/a
18	GATA3	chr1:172501853-172502432	T-47D	breast:	n/a	n/a
19	POLR2A	chr1:172501247-172502720	PANC-1	pancreas:	n/a	n/a
20	YY1	chr1:172501790-172502745	HCT-116	colon:	n/a	chr1:172502194-172502208
21	HDAC2	chr1:172501169-172502748	MCF-7	breast:	n/a	n/a
22	TAF1	chr1:172501150-172502719	SK-N-SH	brain:	n/a	n/a
23	GTF2B	chr1:172502014-172502387	K562	blood:	n/a	n/a
24	MYC	chr1:172501148-172503223	NB4	blood:	n/a	n/a
25	POLR2A	chr1:172500590-172503489	GM12891	blood:	n/a	n/a
26	TAF1	chr1:172501310-172502746	ECC-1	luminal epithelium:	n/a	n/a
27	SP1	chr1:172501129-172502811	HCT-116	colon:	n/a	chr1:172502102-172502112 chr1:172502101-172502113 chr1:172502008-172502020 chr1:172502008-172502020 chr1:172502102-172502112 chr1:172502024-172502036 chr1:172502101-172502113
28	BRCA1	chr1:172501526-172502557	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:172501199-172503014	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr1:172501849-172502764	GM12891	blood:	n/a	n/a
31	HA-E2F1	chr1:172501745-172502646	Hela-S3	cervix:	n/a	chr1:172502135-172502145 chr1:172502199-172502208 chr1:172501919-172501930 chr1:172502028-172502037 chr1:172502208-172502217 chr1:172502275-172502284
32	SPI1	chr1:172501237-172502459	HL-60	blood:	n/a	n/a
33	REST	chr1:172500928-172503498	H1-neurons	neurons:	n/a	chr1:172502117-172502130
34	POLR2A	chr1:172502115-172502483	HepG2	liver:	n/a	n/a
35	TCF7L2	chr1:172501444-172503125	HCT-116	colon:	n/a	n/a
36	MXI1	chr1:172501150-172502712	HepG2	liver:	n/a	n/a
37	WRNIP1	chr1:172501171-172503491	GM12878	blood:	n/a	n/a
38	TAF1	chr1:172501832-172502960	Hela-S3	cervix:	n/a	n/a
39	TBP	chr1:172501135-172503225	K562	blood:	n/a	n/a
40	EP300	chr1:172501330-172502650	GM12878	blood:	n/a	chr1:172502135-172502144
41	MAZ	chr1:172501209-172503393	Hela-S3	cervix:	n/a	n/a
42	PML	chr1:172502137-172502405	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:172501197-172503363	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr1:172501041-172503049	K562	blood:	n/a	n/a
45	ELK1	chr1:172501327-172502792	Hela-S3	cervix:	n/a	n/a
46	ELF1	chr1:172501335-172502652	GM12878	blood:	n/a	chr1:172502019-172502031 chr1:172501949-172501960
47	MAX	chr1:172501235-172502749	K562	blood:	n/a	n/a
48	TCF12	chr1:172501838-172502416	GM12878	blood:	n/a	n/a
49	YY1	chr1:172502021-172502623	GM12891	blood:	n/a	chr1:172502194-172502208
50	GTF2F1	chr1:172501186-172503324	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:172411084..172422561-chr1:172496524..172504623,44	MCF-7	breast:
2	chr1:172502181..172504109-chr1:172575400..172577552,2	K562	blood:
3	chr1:172502150..172502978-chr6:43967876..43968821,2	Hela-S3	cervix:
4	chr1:172501396..172504430-chr1:172536696..172538886,3	MCF-7	breast:
5	chr1:172501784..172502594-chr12:131356402..131357220,2	Hela-S3	cervix:
6	chr1:172502053..172502709-chr2:227700502..227701168,2	NB4	blood:
7	chr1:172502229..172502743-chr17:61904999..61905540,2	Hela-S3	cervix:
8	chr1:172419256..172421468-chr1:172500783..172504604,4	K562	blood:
9	chr1:172502199..172503010-chr19:47248808..47249686,2	NB4	blood:
10	chr1:172502043..172502720-chr22:36850254..36851043,2	Hela-S3	cervix:
11	chr1:172499065..172502708-chr1:172575408..172578949,3	K562	blood:
12	chr1:172502284..172502806-chr7:112090484..112091302,2	Hela-S3	cervix:
13	chr1:172412087..172424934-chr1:172497120..172505334,59	MCF-7	breast:
14	chr1:172410326..172414934-chr1:172499314..172504781,7	K562	blood:
15	chr1:172411064..172415256-chr1:172501216..172504781,6	K562	blood:
16	chr1:172501712..172502368-chr17:56736016..56736733,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGC-4	chr1:172500900-172502606	NONHSAT007615

Variant related genes	Relation type
SUCO	TF binding region
ENSG00000181577	Chromatin interaction
ENSG00000132341	Chromatin interaction
ENSG00000087191	Chromatin interaction
ENSG00000094975	Chromatin interaction
ENSG00000006652	Chromatin interaction
ENSG00000135845	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000228719	Chromatin interaction
ENSG00000108592	Chromatin interaction
ENSG00000181027	Chromatin interaction
ENSG00000090372	Chromatin interaction
ENSG00000144468	Chromatin interaction
ENSG00000180999	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10157501	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911830	0.85[ASN][1000 genomes]
rs10911833	0.84[ASN][1000 genomes]
rs10911843	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10911859	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10911862	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10911875	0.93[ASN][1000 genomes]
rs10911920	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10912075	0.81[AMR][1000 genomes]
rs1159378	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11799659	0.82[ASN][1000 genomes]
rs12021702	0.85[AMR][1000 genomes]
rs12025433	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12038654	0.80[AMR][1000 genomes]
rs12070393	0.84[AMR][1000 genomes]
rs12073872	0.80[ASN][1000 genomes]
rs12093274	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12118647	0.83[ASN][1000 genomes]
rs12120798	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12123755	0.80[AMR][1000 genomes]
rs12130435	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12145007	0.83[ASN][1000 genomes]
rs2239816	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239817	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2285664	0.82[ASN][1000 genomes]
rs2472549	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3738736	0.83[AMR][1000 genomes]
rs3754426	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6424954	0.84[ASN][1000 genomes]
rs6424955	0.85[ASN][1000 genomes]
rs6424956	0.84[ASN][1000 genomes]
rs6424965	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6657023	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6679222	0.84[ASN][1000 genomes]
rs6688929	0.85[ASN][1000 genomes]
rs6691320	0.84[ASN][1000 genomes]
rs6691528	0.84[ASN][1000 genomes]
rs6694111	0.84[ASN][1000 genomes]
rs6697618	0.84[ASN][1000 genomes]
rs6698031	0.84[ASN][1000 genomes]
rs6699802	0.84[ASN][1000 genomes]
rs6702420	0.84[ASN][1000 genomes]
rs72710417	0.85[AMR][1000 genomes]
rs7514814	0.80[AMR][1000 genomes]
rs7517856	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7532580	0.80[AMR][1000 genomes]
rs7542003	0.81[AMR][1000 genomes]
rs9943237	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172500400-172502400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:172500400-172504600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:172500600-172503200	Active TSS	Fetal Thymus	thymus
4	chr1:172500600-172503400	Active TSS	Thymus	Thymus
5	chr1:172500600-172503600	Active TSS	A549	lung
6	chr1:172500600-172503800	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:172500600-172504200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr1:172500600-172504200	Active TSS	NHDF-Ad	bronchial
9	chr1:172500800-172503000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:172500800-172503200	Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr1:172500800-172503200	Active TSS	Fetal Muscle Leg	muscle
12	chr1:172500800-172503400	Active TSS	Primary T cells fromperipheralblood	blood
13	chr1:172500800-172503400	Active TSS	Aorta	Aorta
14	chr1:172500800-172503400	Active TSS	Colon Smooth Muscle	Colon
15	chr1:172500800-172503600	Active TSS	Colonic Mucosa	Colon
16	chr1:172500800-172503800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:172500800-172503800	Active TSS	Fetal Muscle Trunk	muscle
18	chr1:172500800-172504000	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr1:172500800-172504000	Active TSS	Right Ventricle	heart
20	chr1:172500800-172504200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:172500800-172504200	Active TSS	Fetal Stomach	stomach
22	chr1:172500800-172504400	Active TSS	H1 Cell Line	embryonic stem cell
23	chr1:172500800-172504400	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr1:172500800-172504400	Active TSS	HMEC	breast
25	chr1:172500800-172504600	Active TSS	Fetal Brain Female	brain
26	chr1:172500800-172504800	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr1:172501000-172502400	Active TSS	Brain Germinal Matrix	brain
28	chr1:172501000-172502800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr1:172501000-172502800	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr1:172501000-172502800	Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr1:172501000-172503000	Active TSS	Brain Cingulate Gyrus	brain
32	chr1:172501000-172503000	Active TSS	Psoas Muscle	Psoas
33	chr1:172501000-172503200	Active TSS	Primary monocytes fromperipheralblood	blood
34	chr1:172501000-172503200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:172501000-172503200	Active TSS	Duodenum Mucosa	Duodenum
36	chr1:172501000-172503200	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr1:172501000-172503200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr1:172501000-172503200	Active TSS	Rectal Smooth Muscle	rectum
39	chr1:172501000-172503200	Active TSS	Stomach Smooth Muscle	stomach
40	chr1:172501000-172503200	Active TSS	HUVEC	blood vessel
41	chr1:172501000-172503400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:172501000-172503400	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr1:172501000-172503400	Active TSS	Stomach Mucosa	stomach
44	chr1:172501000-172503600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:172501000-172503600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:172501000-172503600	Active TSS	Esophagus	oesophagus
47	chr1:172501000-172503600	Active TSS	Placenta	Placenta
48	chr1:172501000-172503600	Active TSS	Left Ventricle	heart
49	chr1:172501000-172503600	Active TSS	Ovary	ovary
50	chr1:172501000-172503800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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