Variant report

Variant	rs1553300
Chromosome Location	chr13:38923563-38923564
allele	A/C
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	ETS1	chr13:38923516-38924167	GM12878	blood:	n/a	chr13:38923618-38923629 chr13:38923689-38923705
2	E2F4	chr13:38922884-38924685	MCF10A-Er-Src	breast:	n/a	chr13:38923618-38923627
3	POLR2A	chr13:38923434-38923629	HepG2	liver:	n/a	n/a
4	SIN3A	chr13:38923383-38924452	GM12878	blood:	n/a	n/a
5	PBX3	chr13:38923462-38924169	SK-N-SH	brain:	n/a	n/a
6	MXI1	chr13:38923118-38924602	GM12878	blood:	n/a	chr13:38923581-38923596 chr13:38924465-38924474 chr13:38924482-38924491
7	POLR2A	chr13:38923020-38924796	HepG2	liver:	n/a	n/a
8	POLR2A	chr13:38923272-38924545	NB4	blood:	n/a	n/a
9	NFIC	chr13:38923232-38924375	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr13:38923359-38926192	K562	blood:	n/a	n/a
11	SP1	chr13:38923460-38924190	GM12878	blood:	n/a	chr13:38923617-38923626 chr13:38923617-38923627 chr13:38923617-38923626 chr13:38923617-38923627 chr13:38923616-38923628 chr13:38923616-38923628 chr13:38923618-38923627
12	POLR2A	chr13:38923438-38924628	K562	blood:	n/a	n/a
13	SP1	chr13:38923476-38924241	HCT-116	colon:	n/a	chr13:38923617-38923626 chr13:38923617-38923627 chr13:38923617-38923626 chr13:38923617-38923627 chr13:38923616-38923628 chr13:38923616-38923628 chr13:38923618-38923627
14	ELK4	chr13:38923463-38924073	Hela-S3	cervix:	n/a	n/a
15	SP1	chr13:38923410-38924242	A549	lung:	n/a	chr13:38923617-38923626 chr13:38923617-38923627 chr13:38923617-38923626 chr13:38923617-38923627 chr13:38923616-38923628 chr13:38923616-38923628 chr13:38923618-38923627
16	ARID3A	chr13:38923197-38924647	HepG2	liver:	n/a	chr13:38923245-38923261 chr13:38923246-38923262
17	MXI1	chr13:38923153-38924582	HepG2	liver:	n/a	chr13:38923581-38923596 chr13:38924465-38924474 chr13:38924482-38924491
18	MAFK	chr13:38922973-38923584	Hela-S3	cervix:	n/a	n/a
19	MAZ	chr13:38923369-38924553	GM12878	blood:	n/a	chr13:38923623-38923633
20	POLR2A	chr13:38923419-38924609	ProgFib	skin:	n/a	n/a
21	ATF2	chr13:38923548-38924180	GM12878	blood:	n/a	n/a
22	TCF12	chr13:38923465-38924206	A549	lung:	n/a	chr13:38924064-38924073
23	POLR2A	chr13:38923197-38924792	K562	blood:	n/a	n/a
24	STAT3	chr13:38923456-38923586	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr13:38923441-38924500	H1-neurons	neurons:	n/a	n/a
26	POLR2A	chr13:38923333-38923819	GM12892	blood:	n/a	n/a
27	POLR2A	chr13:38923460-38923746	PFSK-1	brain:	n/a	n/a
28	TBP	chr13:38923390-38924189	Hela-S3	cervix:	n/a	n/a
29	MAZ	chr13:38923107-38924549	Hela-S3	cervix:	n/a	chr13:38923623-38923633
30	STAT3	chr13:38923383-38923826	MCF10A-Er-Src	breast:	n/a	chr13:38923613-38923625
31	NFIC	chr13:38923482-38923997	HepG2	liver:	n/a	n/a
32	EP300	chr13:38923060-38924513	K562	blood:	n/a	chr13:38923540-38923549 chr13:38924064-38924074
33	MAX	chr13:38923171-38924713	GM12878	blood:	n/a	chr13:38923623-38923633
34	FOS	chr13:38922941-38923624	MCF10A-Er-Src	breast:	n/a	chr13:38923006-38923018
35	SP4	chr13:38923397-38924205	H1-hESC	embryonic stem cell:	n/a	chr13:38923614-38923630
36	RCOR1	chr13:38923559-38924552	HepG2	liver:	n/a	n/a
37	EGR1	chr13:38923523-38923740	GM12878	blood:	n/a	chr13:38923616-38923630 chr13:38923617-38923627 chr13:38923619-38923632
38	ELF1	chr13:38923388-38924284	MCF-7	breast:	n/a	n/a
39	MAX	chr13:38923480-38924300	SK-N-SH	brain:	n/a	chr13:38923623-38923633
40	REST	chr13:38923303-38924542	H1-neurons	neurons:	n/a	n/a
41	POLR2A	chr13:38922711-38925551	GM12891	blood:	n/a	n/a
42	ELF1	chr13:38923399-38924316	SK-N-SH	brain:	n/a	n/a
43	ELF1	chr13:38923494-38924601	GM12878	blood:	n/a	n/a
44	SIN3AK20	chr13:38923411-38924259	HCT-116	colon:	n/a	n/a
45	MAX	chr13:38923485-38923769	K562	blood:	n/a	chr13:38923623-38923633
46	POLR2A	chr13:38923372-38923722	ECC-1	luminal epithelium:	n/a	n/a
47	SP4	chr13:38923470-38924141	H1-hESC	embryonic stem cell:	n/a	chr13:38923614-38923630
48	GABPA	chr13:38923555-38923734	HepG2	liver:	n/a	chr13:38923618-38923627
49	WRNIP1	chr13:38923096-38924603	GM12878	blood:	n/a	n/a
50	MAX	chr13:38922922-38924882	NB4	blood:	n/a	chr13:38923623-38923633

No.	Distal block	Cell Line	Cell type
1	chr13:38923439..38924342-chr19:36630421..36631091,2	Hela-S3	cervix:
2	chr13:38923147..38923763-chr4:11748300..11748800,2	Hela-S3	cervix:
3	chr10:126604859..126605843-chr13:38923544..38924473,3	NB4	blood:
4	chr13:38903073..38904879-chr13:38922211..38923976,2	K562	blood:
5	chr13:38921186..38924004-chr13:38924043..38925621,2	MCF-7	breast:

Variant related genes	Relation type
UFM1	TF binding region
ENSG00000120686	Chromatin interaction
ENSG00000249456	Chromatin interaction
ENSG00000126247	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10507469	1.00[CHD][hapmap]
rs10514844	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330963	1.00[CHB][hapmap]
rs1330964	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330965	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330976	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1360385	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1576610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1576611	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150468	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231328	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231331	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2231332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455412	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481876	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481877	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485779	1.00[CHD][hapmap]
rs2485783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485788	0.81[EUR][1000 genomes]
rs2485789	1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496456	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496466	1.00[CHB][hapmap]
rs2496473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496476	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943581	0.83[ASN][1000 genomes]
rs4943583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943586	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563608	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563609	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326028	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326913	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332974	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7335723	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338958	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532218	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548320	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603368	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986773	1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9888482	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv869125	chr13:38550449-39132813	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv949406	chr13:38561474-39033484	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv561512	chr13:38881318-38930893	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv900005	chr13:38881318-38932949	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38922400-38925200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr13:38922600-38923600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
3	chr13:38922600-38924800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr13:38922600-38925000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr13:38922600-38925000	Active TSS	K562	blood
6	chr13:38922600-38925200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr13:38922600-38925200	Active TSS	HSMMtube	muscle
8	chr13:38922600-38926000	Active TSS	Right Atrium	heart
9	chr13:38922800-38923600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr13:38922800-38924200	Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr13:38922800-38924400	Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr13:38922800-38924400	Active TSS	Thymus	Thymus
13	chr13:38922800-38924600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:38922800-38924600	Active TSS	Brain Cingulate Gyrus	brain
15	chr13:38922800-38924600	Active TSS	Brain Germinal Matrix	brain
16	chr13:38922800-38924600	Active TSS	Brain Substantia Nigra	brain
17	chr13:38922800-38924600	Active TSS	Rectal Smooth Muscle	rectum
18	chr13:38922800-38924600	Active TSS	Stomach Smooth Muscle	stomach
19	chr13:38922800-38924800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr13:38922800-38924800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr13:38922800-38924800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr13:38922800-38924800	Active TSS	Muscle Satellite Cultured Cells	--
23	chr13:38922800-38924800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr13:38922800-38924800	Active TSS	Fetal Kidney	kidney
25	chr13:38922800-38924800	Active TSS	Fetal Stomach	stomach
26	chr13:38922800-38925000	Active TSS	H1 Cell Line	embryonic stem cell
27	chr13:38922800-38925000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr13:38922800-38925000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr13:38922800-38925000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr13:38922800-38925000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr13:38922800-38925000	Active TSS	Aorta	Aorta
32	chr13:38922800-38925000	Active TSS	Fetal Intestine Large	intestine
33	chr13:38922800-38925000	Active TSS	GM12878-XiMat	blood
34	chr13:38922800-38925200	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr13:38922800-38925200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr13:38922800-38925200	Active TSS	NHLF	lung
37	chr13:38922800-38926200	Active TSS	Right Ventricle	heart
38	chr13:38923000-38923600	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr13:38923000-38923600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr13:38923000-38924400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr13:38923000-38924400	Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr13:38923000-38924600	Active TSS	Brain Anterior Caudate	brain
43	chr13:38923000-38924600	Active TSS	Colon Smooth Muscle	Colon
44	chr13:38923000-38924600	Active TSS	Fetal Heart	heart
45	chr13:38923000-38924800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr13:38923000-38924800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr13:38923000-38924800	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr13:38923000-38924800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr13:38923000-38924800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr13:38923000-38924800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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