Variant report

Variant	rs9545126
Chromosome Location	chr13:80057681-80057682
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	FOS	chr13:80057536-80057764	MCF10A-Er-Src	breast:	n/a	chr13:80057704-80057714 chr13:80057704-80057714 chr13:80057704-80057714
2	FOS	chr13:80057609-80057875	MCF10A-Er-Src	breast:	n/a	chr13:80057704-80057714 chr13:80057704-80057714 chr13:80057704-80057714
3	POLR2A	chr13:80054410-80058154	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr13:80057481-80058200	MCF10A-Er-Src	breast:	n/a	chr13:80058028-80058036 chr13:80058026-80058037
5	MAFK	chr13:80057354-80057720	HepG2	liver:	n/a	chr13:80057532-80057543
6	MAFK	chr13:80057361-80057778	Hela-S3	cervix:	n/a	chr13:80057532-80057543
7	POLR2A	chr13:80057584-80057754	A549	lung:	n/a	n/a
8	MAFF	chr13:80057359-80057730	HepG2	liver:	n/a	n/a
9	MAFK	chr13:80057358-80057726	HepG2	liver:	n/a	chr13:80057532-80057543
10	POLR2A	chr13:80057467-80057853	Hela-S3	cervix:	n/a	n/a
11	STAT3	chr13:80057294-80058206	MCF10A-Er-Src	breast:	n/a	chr13:80058028-80058036 chr13:80058026-80058037
12	E2F4	chr13:80057367-80057699	MCF10A-Er-Src	breast:	n/a	n/a
13	MAFK	chr13:80057360-80057722	K562	blood:	n/a	chr13:80057532-80057543
14	POLR2A	chr13:80057124-80057873	K562	blood:	n/a	n/a
15	MAFF	chr13:80057326-80057719	K562	blood:	n/a	n/a
16	CEBPB	chr13:80057266-80057945	IMR90	lung:	n/a	chr13:80057440-80057451
17	STAT3	chr13:80057355-80058206	MCF10A-Er-Src	breast:	n/a	chr13:80058028-80058036 chr13:80058026-80058037
18	POLR2A	chr13:80054586-80058161	MCF10A-Er-Src	breast:	n/a	n/a
19	MAFK	chr13:80057285-80057813	IMR90	lung:	n/a	chr13:80057532-80057543
20	STAT3	chr13:80057366-80058197	MCF10A-Er-Src	breast:	n/a	chr13:80058028-80058036 chr13:80058026-80058037
21	FOS	chr13:80057458-80058196	MCF10A-Er-Src	breast:	n/a	chr13:80057704-80057714 chr13:80057704-80057714 chr13:80057704-80057714
22	FOS	chr13:80057416-80058126	MCF10A-Er-Src	breast:	n/a	chr13:80057704-80057714 chr13:80057704-80057714 chr13:80057704-80057714

No.	Distal block	Cell Line	Cell type
1	chr13:80054400..80056939-chr13:80057406..80059171,2	MCF-7	breast:
2	chr13:79977332..79980292-chr13:80055643..80057700,2	K562	blood:
3	chr13:80057193..80059999-chr13:80114272..80116741,2	K562	blood:
4	chr13:80056153..80058862-chr13:80062367..80066425,4	K562	blood:

Variant related genes	Relation type
NDFIP2-AS1	TF binding region
ENSG00000102471	Chromatin interaction
ENSG00000232132	Chromatin interaction
ENSG00000139746	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11549502	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11838769	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11839222	0.89[AMR][1000 genomes]
rs11840407	1.00[CHB][hapmap]
rs17071629	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17431002	1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs4884132	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4885635	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4885639	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4885641	0.84[EUR][1000 genomes]
rs6563111	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs67435118	0.85[AMR][1000 genomes]
rs7321672	0.89[AMR][1000 genomes]
rs73234683	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73234690	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73235960	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7337908	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs7338662	1.00[CHB][hapmap]
rs7399942	0.81[EUR][1000 genomes]
rs7983288	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7983516	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7990729	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7991663	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7992646	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs8000301	0.87[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9530926	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9530927	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];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9530928	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9530932	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9530933	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9530935	0.81[EUR][1000 genomes]
rs9530936	0.84[EUR][1000 genomes]
rs9545119	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9545127	0.85[CEU][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9545129	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];0.98[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9545130	0.85[CEU][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9545132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9545140	0.81[EUR][1000 genomes]
rs9545141	0.81[EUR][1000 genomes]
rs9545143	0.84[EUR][1000 genomes]
rs9545144	0.81[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	nsv832657	chr13:79904978-80099108	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv523979	chr13:79979679-80120263	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80054800-80057800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr13:80054800-80057800	Active TSS	Fetal Intestine Large	intestine
3	chr13:80054800-80057800	Active TSS	Fetal Intestine Small	intestine
4	chr13:80054800-80058000	Active TSS	Duodenum Mucosa	Duodenum
5	chr13:80054800-80059400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr13:80055800-80057800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr13:80056000-80058800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr13:80056200-80057800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr13:80056200-80058000	Enhancers	Stomach Mucosa	stomach
10	chr13:80056200-80058000	Flanking Active TSS	NH-A	brain
11	chr13:80056200-80058800	Weak transcription	Small Intestine	intestine
12	chr13:80056200-80059200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr13:80056200-80060600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr13:80056200-80060800	Weak transcription	Gastric	stomach
15	chr13:80056200-80063200	Weak transcription	Left Ventricle	heart
16	chr13:80056200-80066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr13:80056200-80066600	Weak transcription	Psoas Muscle	Psoas
18	chr13:80056200-80077400	Weak transcription	Right Ventricle	heart
19	chr13:80056400-80057800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr13:80056400-80058000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr13:80056400-80058000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr13:80056400-80058000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr13:80056600-80057800	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr13:80056600-80057800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr13:80056600-80057800	Flanking Active TSS	Hela-S3	cervix
26	chr13:80056600-80058000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr13:80056600-80058000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr13:80056600-80058000	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr13:80056600-80058600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr13:80056600-80064200	Weak transcription	Placenta	Placenta
31	chr13:80056800-80057800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr13:80056800-80057800	Enhancers	Fetal Kidney	kidney
33	chr13:80056800-80058000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr13:80056800-80058000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr13:80056800-80058000	Enhancers	Brain Cingulate Gyrus	brain
36	chr13:80056800-80058000	Flanking Active TSS	NHDF-Ad	bronchial
37	chr13:80056800-80058800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr13:80056800-80059200	Weak transcription	Pancreas	Pancrea
39	chr13:80056800-80059600	Enhancers	Brain Hippocampus Middle	brain
40	chr13:80056800-80059600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr13:80056800-80061200	Enhancers	Fetal Heart	heart
42	chr13:80056800-80064000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr13:80056800-80064400	Weak transcription	Fetal Stomach	stomach
44	chr13:80056800-80065800	Weak transcription	Fetal Muscle Leg	muscle
45	chr13:80057000-80057800	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr13:80057000-80058000	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr13:80057000-80058000	Flanking Active TSS	Osteobl	bone
48	chr13:80057000-80058400	Enhancers	K562	blood
49	chr13:80057000-80058800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr13:80057000-80058800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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