Variant report

Variant	rs2296573
Chromosome Location	chr13:48575587-48575588
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:296)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:296 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr13:48575520-48575670	GM12871	blood:	n/a	n/a
2	MYC	chr13:48575237-48576085	A549	lung:	n/a	n/a
3	RAD21	chr13:48574956-48575709	IMR90	lung:	n/a	n/a
4	POLR2A	chr13:48574875-48575763	ECC-1	luminal epithelium:	n/a	n/a
5	YY1	chr13:48574944-48575650	K562	blood:	n/a	chr13:48575082-48575096 chr13:48575430-48575444 chr13:48575462-48575476 chr13:48575431-48575445
6	POLR2A	chr13:48575095-48575731	PFSK-1	brain:	n/a	n/a
7	MAFK	chr13:48575303-48575829	Hela-S3	cervix:	n/a	n/a
8	SP4	chr13:48575217-48575636	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr13:48575384-48575907	HepG2	liver:	n/a	n/a
10	POLR2A	chr13:48575132-48575872	HepG2	liver:	n/a	n/a
11	POLR2A	chr13:48575031-48575824	GM12892	blood:	n/a	n/a
12	CTCF	chr13:48575580-48575730	GM12870	blood:	n/a	n/a
13	POLR2A	chr13:48575071-48575764	K562	blood:	n/a	n/a
14	BHLHE40	chr13:48575414-48575722	GM12878	blood:	n/a	n/a
15	CTCF	chr13:48575480-48575630	AG04449	skin:	n/a	n/a
16	TEAD4	chr13:48575240-48575596	H1-hESC	embryonic stem cell:	n/a	n/a
17	TFAP2C	chr13:48574861-48576517	Hela-S3	cervix:	n/a	chr13:48575177-48575192
18	SMC3	chr13:48575582-48575636	GM12878	blood:	n/a	n/a
19	SIN3AK20	chr13:48575150-48575658	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr13:48575021-48575680	GM12878	blood:	n/a	n/a
21	POLR2A	chr13:48575017-48575856	HUVEC	blood vessel:	n/a	n/a
22	TCF7L2	chr13:48575208-48576583	Hela-S3	cervix:	n/a	n/a
23	NRF1	chr13:48575162-48575663	GM12878	blood:	n/a	chr13:48575437-48575448 chr13:48575467-48575478 chr13:48575437-48575446 chr13:48575432-48575441 chr13:48575437-48575451 chr13:48575434-48575448 chr13:48575436-48575447
24	MAX	chr13:48575300-48575892	A549	lung:	n/a	n/a
25	YY1	chr13:48574822-48575665	SK-N-SH_RA	brain:	n/a	chr13:48575082-48575096 chr13:48575430-48575444 chr13:48575462-48575476 chr13:48575431-48575445
26	SIN3A	chr13:48574989-48575596	GM12878	blood:	n/a	n/a
27	FOXP2	chr13:48575351-48575674	SK-N-MC	brain:	n/a	n/a
28	TCF7L2	chr13:48575284-48576033	PANC-1	pancreas:	n/a	n/a
29	PML	chr13:48574967-48575733	GM12878	blood:	n/a	n/a
30	POLR2A	chr13:48575112-48575815	PANC-1	pancreas:	n/a	n/a
31	TBP	chr13:48575220-48575733	K562	blood:	n/a	n/a
32	POLR2A	chr13:48575097-48575790	GM15510	blood:	n/a	n/a
33	RFX5	chr13:48575286-48575839	HepG2	liver:	n/a	n/a
34	CTCF	chr13:48575500-48575650	GM12868	blood:	n/a	n/a
35	POLR2A	chr13:48574934-48575852	HL-60	blood:	n/a	n/a
36	POLR2A	chr13:48575039-48575677	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr13:48575226-48575721	Hela-S3	cervix:	n/a	n/a
38	RAD21	chr13:48575406-48575920	Hela-S3	cervix:	n/a	n/a
39	MAZ	chr13:48575237-48575749	K562	blood:	n/a	n/a
40	POLR2A	chr13:48575107-48575859	Raji	blood:	n/a	n/a
41	POLR2A	chr13:48575081-48575980	A549	lung:	n/a	n/a
42	POLR2A	chr13:48575076-48576020	Hela-S3	cervix:	n/a	n/a
43	TFAP2A	chr13:48574863-48575811	Hela-S3	cervix:	n/a	chr13:48575182-48575190 chr13:48575179-48575193
44	POLR2A	chr13:48574838-48576045	HepG2	liver:	n/a	n/a
45	SIN3AK20	chr13:48574704-48575992	MCF-7	breast:	n/a	n/a
46	CTCF	chr13:48575480-48575630	GM06990	blood:	n/a	n/a
47	RCOR1	chr13:48575248-48575994	Hela-S3	cervix:	n/a	n/a
48	TAF1	chr13:48575112-48575767	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr13:48574980-48575757	GM19099	blood:	n/a	n/a
50	CTCF	chr13:48575460-48575610	AG04449	skin:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:48575574-48575624	PrEC	prostate:	n/a
2	chr13:48575574-48575624	RPTEC	kidney:	n/a
3	chr13:48575574-48575624	HIPEpiC	eye:	n/a
4	chr13:48575574-48575624	NB4	blood:	n/a
5	chr13:48575574-48575624	HepG2	liver:	n/a
6	chr13:48575574-48575624	HPAEpiC	pulmonary alveolar:	n/a
7	chr13:48575574-48575624	T-47D	breast:	n/a
8	chr13:48575574-48575624	HAEpiC	amniotic membrane:	n/a
9	chr13:48575574-48575624	SAEC	small airway:	n/a
10	chr13:48575574-48575624	GM12878	blood:	n/a
11	chr13:48575574-48575624	H1-hESC	embryonic stem cell:	embryo
12	chr13:48575574-48575624	PFSK-1	brain:	n/a
13	chr13:48575574-48575624	SK-N-SH	brain:	n/a
14	chr13:48575574-48575624	HNPCEpiC	eye:	n/a
15	chr13:48575574-48575624	HEK293	kidney:	embryo
16	chr13:48575574-48575624	HCT-116	colon:	n/a
17	chr13:48575574-48575624	NHBE	bronchial:	n/a
18	chr13:48575574-48575624	GM19239	blood:	n/a
19	chr13:48575574-48575624	AG09309	skin:	n/a
20	chr13:48575574-48575624	NHDF-neo	bronchial:	n/a
21	chr13:48575574-48575624	Hepatocyte	liver:	n/a
22	chr13:48575574-48575624	HL-60	blood:	n/a
23	chr13:48575574-48575624	CMK	blood:	n/a
24	chr13:48575574-48575624	A549	lung:	n/a
25	chr13:48575574-48575624	MCF10A-Er-Src	breast:	n/a
26	chr13:48575574-48575624	Caco-2	colon:	n/a
27	chr13:48575574-48575624	HEEpiC	esophagus:	n/a
28	chr13:48575574-48575624	SKMC	muscle:	n/a
29	chr13:48575574-48575624	U87	brain:	n/a
30	chr13:48575574-48575624	Hela-S3	cervix:	n/a
31	chr13:48575574-48575624	Jurkat	blood:	n/a
32	chr13:48575574-48575624	HCPEpiC	choroid plexus:	n/a
33	chr13:48575574-48575624	AG04450	lung:	fetal
34	chr13:48575574-48575624	AG04449	skin:	fetal
35	chr13:48575574-48575624	NT2-D1	testis:	n/a
36	chr13:48575574-48575624	AoSMC	blood vessel:	n/a
37	chr13:48575574-48575624	HRPEpiC	eye:	n/a
38	chr13:48575574-48575624	GM12892	blood:	n/a
39	chr13:48575574-48575624	AG10803	skin:	n/a
40	chr13:48575574-48575624	HCM	heart:	n/a
41	chr13:48575574-48575624	NH-A	brain:	n/a
42	chr13:48575574-48575624	AG09319	gingival:	n/a
43	chr13:48575574-48575624	HRE	kidney:	n/a
44	chr13:48575574-48575624	IMR90	lung:	fetal
45	chr13:48575574-48575624	BJ	skin:	n/a
46	chr13:48575574-48575624	GM06990	blood:	n/a
47	chr13:48575574-48575624	HUVEC	blood vessel:	n/a
48	chr13:48575574-48575624	ovcar-3	ovarian:	n/a
49	chr13:48575574-48575624	K562	blood:	n/a
50	chr13:48575574-48575624	ProgFib	skin:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:48573666..48577274-chr13:48610467..48613685,4	MCF-7	breast:
2	chr13:48574996..48575645-chr17:49243449..49244132,2	HCT-116	colon:
3	chr11:62608655..62609644-chr13:48575146..48575728,2	NB4	blood:
4	chr13:48573863..48576384-chr13:48611584..48613293,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NUDT15-2	chr13:48575525-48575958	ENSG00000227848.1

No data

Variant related genes	Relation type
SUCLA2	TF binding region
SUCLA2	CpG island
ENSG00000243678	Chromatin interaction
ENSG00000136143	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000136159	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11148100	0.85[AFR][1000 genomes]
rs11618397	0.80[YRI][hapmap]
rs12584652	0.84[EUR][1000 genomes]
rs12860399	0.87[EUR][1000 genomes]
rs12864691	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1326136	0.80[YRI][hapmap]
rs1326140	0.80[YRI][hapmap]
rs1536301	0.80[YRI][hapmap]
rs17350996	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs17425881	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2031590	0.87[AFR][1000 genomes]
rs2031591	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2148244	0.82[AFR][1000 genomes]
rs2296574	0.80[YRI][hapmap]
rs4245347	0.82[AFR][1000 genomes]
rs4522322	0.83[AFR][1000 genomes]
rs4942728	0.87[AFR][1000 genomes]
rs4942730	0.87[AFR][1000 genomes]
rs4942747	0.90[TSI][hapmap]
rs7317860	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7318770	0.96[YRI][hapmap]
rs7320366	0.80[YRI][hapmap]
rs7323277	0.82[ASN][1000 genomes]
rs7326889	0.82[AFR][1000 genomes]
rs7328525	0.81[AFR][1000 genomes]
rs7328537	0.81[AFR][1000 genomes]
rs7330472	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7331900	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7334463	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7337766	0.82[CHB][hapmap]
rs7338125	0.80[YRI][hapmap]
rs765809	0.80[YRI][hapmap]
rs7981114	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs7981260	0.83[ASN][1000 genomes]
rs7989231	0.86[YRI][hapmap]
rs7994427	0.82[ASN][1000 genomes]
rs7996580	0.89[LWK][hapmap];0.93[YRI][hapmap]
rs7997802	0.93[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7998116	0.93[YRI][hapmap]
rs7998260	0.87[AFR][1000 genomes]
rs7998497	0.84[AFR][1000 genomes]
rs8000164	0.87[AFR][1000 genomes]
rs8001432	0.84[AFR][1000 genomes]
rs8001871	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9316339	0.80[YRI][hapmap]
rs9316346	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs9316348	0.90[TSI][hapmap]
rs9316349	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs9526422	0.84[AFR][1000 genomes]
rs9526429	0.80[YRI][hapmap]
rs9534877	0.80[YRI][hapmap]
rs9534878	0.80[YRI][hapmap]
rs9534889	0.80[YRI][hapmap]
rs9534903	0.83[AFR][1000 genomes]
rs9534904	0.86[YRI][hapmap]
rs9534905	0.93[YRI][hapmap]
rs9534906	0.93[YRI][hapmap]
rs9534929	0.88[YRI][hapmap]
rs9562779	0.82[ASN][1000 genomes]
rs9567958	1.00[YRI][hapmap]
rs9567960	0.80[YRI][hapmap]
rs9567964	0.82[AFR][1000 genomes]
rs9567965	0.87[EUR][1000 genomes]
rs9567968	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9567979	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9567980	0.92[YRI][hapmap]
rs9595813	0.83[ASN][1000 genomes]
rs9595825	0.80[YRI][hapmap]
rs9595835	0.90[TSI][hapmap]

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	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2296573	MED4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48573000-48576600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr13:48573600-48576200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr13:48573800-48575600	Active TSS	Duodenum Mucosa	Duodenum
4	chr13:48573800-48576400	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr13:48574000-48575600	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr13:48574000-48575600	Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr13:48574000-48575600	Active TSS	GM12878-XiMat	blood
8	chr13:48574000-48575600	Active TSS	K562	blood
9	chr13:48574000-48576000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr13:48574000-48576000	Active TSS	Psoas Muscle	Psoas
11	chr13:48574000-48576000	Active TSS	Right Atrium	heart
12	chr13:48574000-48576200	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr13:48574200-48575600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr13:48574200-48575600	Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr13:48574200-48575600	Active TSS	HMEC	breast
16	chr13:48574200-48575600	Active TSS	NHDF-Ad	bronchial
17	chr13:48574200-48575800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr13:48574200-48575800	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr13:48574200-48575800	ZNF genes & repeats	Fetal Brain Male	brain
20	chr13:48574200-48575800	Active TSS	HSMM	muscle
21	chr13:48574200-48576000	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr13:48574200-48576000	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr13:48574200-48576000	Active TSS	Ovary	ovary
24	chr13:48574200-48576200	Active TSS	Fetal Brain Female	brain
25	chr13:48574200-48576200	Active TSS	A549	lung
26	chr13:48574200-48576400	Active TSS	Brain Germinal Matrix	brain
27	chr13:48574400-48575600	Active TSS	HSMMtube	muscle
28	chr13:48574400-48575600	Active TSS	NHEK	skin
29	chr13:48574400-48575800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr13:48574400-48575800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr13:48574400-48575800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr13:48574400-48575800	Active TSS	Colon Smooth Muscle	Colon
33	chr13:48574400-48575800	Active TSS	Fetal Intestine Small	intestine
34	chr13:48574400-48575800	Active TSS	Left Ventricle	heart
35	chr13:48574400-48575800	Active TSS	Right Ventricle	heart
36	chr13:48574400-48576000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr13:48574400-48576000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr13:48574400-48576000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr13:48574400-48576000	Active TSS	Aorta	Aorta
40	chr13:48574400-48576000	Active TSS	Esophagus	oesophagus
41	chr13:48574400-48576000	Active TSS	Fetal Muscle Trunk	muscle
42	chr13:48574400-48576200	Active TSS	H9 Cell Line	embryonic stem cell
43	chr13:48574400-48576200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr13:48574600-48575600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr13:48574600-48575600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr13:48574600-48575600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr13:48574600-48575600	Active TSS	Fetal Intestine Large	intestine
48	chr13:48574600-48575600	Active TSS	Fetal Muscle Leg	muscle
49	chr13:48574600-48575600	Active TSS	Placenta	Placenta
50	chr13:48574600-48575600	Active TSS	Fetal Stomach	stomach

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