Variant report

Variant	rs980988
Chromosome Location	chr4:54244438-54244439
allele	G/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	chr4:54243462-54244508	GM12891	blood:	n/a	n/a
2	ELF1	chr4:54243555-54244472	GM12878	blood:	n/a	chr4:54243762-54243771
3	ZNF384	chr4:54244343-54244439	GM12878	blood:	n/a	n/a
4	MAX	chr4:54243287-54244774	NB4	blood:	n/a	chr4:54243636-54243646
5	RAD21	chr4:54243436-54244447	IMR90	lung:	n/a	n/a
6	MXI1	chr4:54243504-54244491	HepG2	liver:	n/a	n/a
7	MAZ	chr4:54243356-54244800	IMR90	lung:	n/a	chr4:54243636-54243646
8	ZMIZ1	chr4:54243450-54244476	K562	blood:	n/a	n/a
9	POLR2A	chr4:54243472-54244527	GM12892	blood:	n/a	n/a
10	POLR2A	chr4:54243457-54244498	GM18526	blood:	n/a	n/a
11	E2F6	chr4:54243611-54244465	H1-hESC	embryonic stem cell:	n/a	chr4:54243732-54243741 chr4:54243638-54243647 chr4:54243638-54243650
12	SIN3AK20	chr4:54243736-54244486	SK-N-SH	brain:	n/a	n/a
13	MAX	chr4:54243417-54244523	SK-N-SH	brain:	n/a	chr4:54243636-54243646
14	POLR2A	chr4:54243544-54244484	GM12878	blood:	n/a	n/a
15	SMC3	chr4:54243262-54244468	Hela-S3	cervix:	n/a	n/a
16	MAX	chr4:54243459-54244511	ECC-1	luminal epithelium:	n/a	chr4:54243636-54243646
17	PAX5	chr4:54243595-54244440	GM12892	blood:	n/a	n/a
18	MYC	chr4:54243459-54244651	NB4	blood:	n/a	chr4:54243636-54243646
19	CCNT2	chr4:54243585-54244443	K562	blood:	n/a	chr4:54243638-54243647 chr4:54243711-54243720
20	POLR2A	chr4:54243437-54244565	Hela-S3	cervix:	n/a	n/a
21	ZNF263	chr4:54243648-54244455	HEK293-T-REx	kidney:	n/a	n/a
22	MXI1	chr4:54243000-54245752	SK-N-SH	brain:	n/a	n/a
23	MAX	chr4:54243478-54244491	HepG2	liver:	n/a	chr4:54243636-54243646
24	POLR2A	chr4:54243462-54244522	GM19193	blood:	n/a	n/a
25	REST	chr4:54243090-54244588	H1-neurons	neurons:	n/a	n/a
26	MAX	chr4:54243533-54244472	K562	blood:	n/a	chr4:54243636-54243646
27	SIN3A	chr4:54243537-54244518	GM12878	blood:	n/a	n/a
28	RCOR1	chr4:54244418-54244529	HepG2	liver:	n/a	n/a
29	CREB1	chr4:54243428-54244545	HepG2	liver:	n/a	n/a
30	POLR2A	chr4:54243434-54244452	HL-60	blood:	n/a	n/a
31	MAX	chr4:54243398-54244561	A549	lung:	n/a	chr4:54243636-54243646
32	POLR2A	chr4:54243408-54244462	K562	blood:	n/a	n/a
33	POLR2A	chr4:54244198-54244492	GM12891	blood:	n/a	n/a
34	PML	chr4:54243289-54244689	GM12878	blood:	n/a	n/a
35	MAX	chr4:54243452-54244571	K562	blood:	n/a	chr4:54243636-54243646
36	MAX	chr4:54243552-54244460	H1-hESC	embryonic stem cell:	n/a	chr4:54243636-54243646
37	SIN3AK20	chr4:54243587-54244451	K562	blood:	n/a	n/a
38	UBTF	chr4:54243526-54244560	K562	blood:	n/a	n/a
39	MAX	chr4:54243349-54244543	Hela-S3	cervix:	n/a	chr4:54243636-54243646
40	MAX	chr4:54243389-54244570	HCT-116	colon:	n/a	chr4:54243636-54243646
41	MAX	chr4:54243509-54244531	A549	lung:	n/a	chr4:54243636-54243646
42	POLR2A	chr4:54243474-54244534	GM12891	blood:	n/a	n/a
43	POLR2A	chr4:54243458-54244516	GM12878	blood:	n/a	n/a
44	MAX	chr4:54243500-54244462	MCF-7	breast:	n/a	chr4:54243636-54243646
45	HA-E2F1	chr4:54243467-54244449	MCF-7	breast:	n/a	chr4:54243732-54243741 chr4:54243638-54243647 chr4:54243638-54243650
46	MXI1	chr4:54243427-54244552	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr4:54243462-54244530	GM15510	blood:	n/a	n/a
48	POLR2A	chr4:54242979-54244534	GM12891	blood:	n/a	n/a
49	RUNX3	chr4:54243557-54244625	GM12878	blood:	n/a	n/a
50	ZNF274	chr4:54243939-54244536	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:54231262..54233846-chr4:54243717..54245288,2	MCF-7	breast:
2	chr4:54230756..54233682-chr4:54240977..54245711,5	MCF-7	breast:
3	chr4:54231892..54232556-chr4:54243887..54244579,2	MCF-7	breast:

Variant related genes	Relation type
FIP1L1	TF binding region
ENSG00000184178	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10012853	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10013573	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10028214	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1014056	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10517296	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133267	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11935822	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11942086	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11946199	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12499401	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12507723	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13120051	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13125807	0.84[ASN][1000 genomes]
rs13130836	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1351514	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17082659	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17082910	0.81[ASN][1000 genomes]
rs2128103	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2170421	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271555	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292579	0.81[ASN][1000 genomes]
rs34028346	0.80[ASN][1000 genomes]
rs34173240	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34317954	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35033239	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35089532	0.81[ASN][1000 genomes]
rs35225781	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35313782	0.80[ASN][1000 genomes]
rs3817270	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3946758	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3986364	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6420001	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554095	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554096	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554102	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6554103	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554108	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6846569	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6847289	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71597836	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678953	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7679743	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7684450	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7684894	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7694840	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997832	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992820	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9997358	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9997844	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs980988	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54243000-54244800	Active TSS	Fetal Lung	lung
2	chr4:54243000-54244800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr4:54243000-54245000	Active TSS	Brain Cingulate Gyrus	brain
4	chr4:54243000-54247800	Active TSS	GM12878-XiMat	blood
5	chr4:54243200-54244600	Active TSS	Rectal Smooth Muscle	rectum
6	chr4:54243200-54244600	Active TSS	Sigmoid Colon	Sigmoid Colon
7	chr4:54243200-54244800	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr4:54243200-54244800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr4:54243200-54244800	Active TSS	Fetal Muscle Trunk	muscle
10	chr4:54243200-54244800	Active TSS	NHEK	skin
11	chr4:54243200-54245000	Active TSS	H9 Cell Line	embryonic stem cell
12	chr4:54243200-54245200	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr4:54243200-54245200	Active TSS	Fetal Intestine Small	intestine
14	chr4:54243200-54245200	Active TSS	Fetal Stomach	stomach
15	chr4:54243200-54245400	Active TSS	H1 Cell Line	embryonic stem cell
16	chr4:54243200-54245400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:54243200-54245400	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr4:54243200-54245400	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr4:54243200-54245400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:54243200-54245400	Active TSS	Psoas Muscle	Psoas
21	chr4:54243200-54245400	Active TSS	Right Ventricle	heart
22	chr4:54243200-54245600	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr4:54243200-54245800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:54243200-54246000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:54243200-54246200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:54243200-54246200	Active TSS	Ovary	ovary
27	chr4:54243200-54246200	Active TSS	Thymus	Thymus
28	chr4:54243200-54246400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:54243400-54244600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:54243400-54244600	Active TSS	Liver	Liver
31	chr4:54243400-54244600	Active TSS	Brain Angular Gyrus	brain
32	chr4:54243400-54244600	Active TSS	Brain Substantia Nigra	brain
33	chr4:54243400-54244600	Active TSS	Colon Smooth Muscle	Colon
34	chr4:54243400-54244600	Active TSS	Duodenum Mucosa	Duodenum
35	chr4:54243400-54244600	Active TSS	Fetal Brain Female	brain
36	chr4:54243400-54244600	Active TSS	Small Intestine	intestine
37	chr4:54243400-54244800	Active TSS	Primary B cells from peripheral blood	blood
38	chr4:54243400-54244800	Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr4:54243400-54244800	Active TSS	Brain Anterior Caudate	brain
40	chr4:54243400-54244800	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr4:54243400-54244800	Active TSS	Fetal Brain Male	brain
42	chr4:54243400-54244800	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr4:54243400-54245000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr4:54243400-54245000	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr4:54243400-54245000	Active TSS	Primary T cells fromperipheralblood	blood
46	chr4:54243400-54245000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:54243400-54245000	Active TSS	Colonic Mucosa	Colon
48	chr4:54243400-54245000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr4:54243400-54245000	Active TSS	Fetal Muscle Leg	muscle
50	chr4:54243400-54245000	Active TSS	Placenta	Placenta

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