Variant report

Variant	rs972297
Chromosome Location	chr13:49789164-49789165
allele	A/G
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	NFIC	chr13:49788982-49789569	HepG2	liver:	n/a	n/a
2	MAX	chr13:49789072-49789638	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr13:49789163-49789487	HCT-116	colon:	n/a	n/a
4	GABPA	chr13:49789010-49789696	HL-60	blood:	n/a	n/a
5	CTCF	chr13:49789140-49789290	RPTEC	kidney:	n/a	n/a
6	MAFF	chr13:49789042-49789350	HepG2	liver:	n/a	chr13:49789159-49789177
7	MYC	chr13:49787737-49789657	NB4	blood:	n/a	n/a
8	GABPA	chr13:49789129-49789570	MCF-7	breast:	n/a	n/a
9	EBF1	chr13:49789096-49789443	GM12878	blood:	n/a	n/a
10	RAD21	chr13:49789154-49789459	H1-hESC	embryonic stem cell:	n/a	chr13:49789316-49789335 chr13:49789321-49789331 chr13:49789321-49789333
11	CTCF	chr13:49789160-49789310	GM12864	blood:	n/a	n/a
12	CEBPB	chr13:49788808-49789551	HepG2	liver:	n/a	chr13:49789099-49789112 chr13:49789100-49789111
13	MYBL2	chr13:49788925-49789491	HepG2	liver:	n/a	n/a
14	CEBPB	chr13:49789142-49789583	MCF-7	breast:	n/a	n/a
15	MAX	chr13:49789155-49789640	ECC-1	luminal epithelium:	n/a	n/a
16	TEAD4	chr13:49788917-49789538	HepG2	liver:	n/a	n/a
17	HEY1	chr13:49788995-49789541	HepG2	liver:	n/a	chr13:49789441-49789450
18	CEBPB	chr13:49788971-49789443	HepG2	liver:	n/a	chr13:49789099-49789112 chr13:49789100-49789111
19	MAX	chr13:49788704-49789733	HepG2	liver:	n/a	n/a
20	POLR2A	chr13:49787122-49789611	Hela-S3	cervix:	n/a	n/a
21	MAX	chr13:49789114-49789687	ECC-1	luminal epithelium:	n/a	n/a
22	SMC3	chr13:49788859-49789424	HepG2	liver:	n/a	chr13:49789317-49789331
23	MBD4	chr13:49788849-49789617	HepG2	liver:	n/a	n/a
24	ATF2	chr13:49789033-49789496	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr13:49787721-49789664	NB4	blood:	n/a	n/a
26	MAX	chr13:49789027-49789638	HCT-116	colon:	n/a	n/a
27	ELF1	chr13:49788991-49789620	HepG2	liver:	n/a	chr13:49789364-49789373
28	MAFK	chr13:49788957-49789416	HepG2	liver:	n/a	chr13:49789157-49789173
29	MAX	chr13:49788814-49789743	HepG2	liver:	n/a	n/a
30	CTCF	chr13:49789120-49789270	A549	lung:	n/a	n/a
31	CTCF	chr13:49789120-49789270	HEEpiC	esophagus:	n/a	n/a
32	ELF1	chr13:49789118-49789658	MCF-7	breast:	n/a	chr13:49789364-49789373
33	MYBL2	chr13:49788859-49789580	HepG2	liver:	n/a	n/a
34	CTCF	chr13:49789020-49789170	HCPEpiC	choroid plexus:	n/a	n/a
35	POLR2A	chr13:49788117-49789450	Hela-S3	cervix:	n/a	n/a
36	GABPA	chr13:49789051-49789604	MCF-7	breast:	n/a	n/a
37	POLR2A	chr13:49788862-49789667	HepG2	liver:	n/a	n/a
38	MAX	chr13:49789027-49789703	HCT-116	colon:	n/a	n/a
39	MAZ	chr13:49789162-49789469	Hela-S3	cervix:	n/a	n/a
40	HEY1	chr13:49789063-49789494	HepG2	liver:	n/a	chr13:49789441-49789450
41	POLR2A	chr13:49789127-49789420	HCT-116	colon:	n/a	n/a
42	EP300	chr13:49788961-49789396	HepG2	liver:	n/a	n/a
43	CEBPB	chr13:49788951-49789530	H1-hESC	embryonic stem cell:	n/a	chr13:49789099-49789112 chr13:49789100-49789111
44	POLR2A	chr13:49788862-49789285	GM12878	blood:	n/a	n/a
45	WRNIP1	chr13:49789104-49789546	GM12878	blood:	n/a	n/a
46	SPI1	chr13:49788801-49789672	HL-60	blood:	n/a	chr13:49789235-49789248 chr13:49789363-49789376
47	MAX	chr13:49789065-49789651	H1-hESC	embryonic stem cell:	n/a	n/a
48	GABPA	chr13:49788820-49789834	HL-60	blood:	n/a	n/a
49	CTCF	chr13:49789039-49789443	H1-hESC	embryonic stem cell:	n/a	chr13:49789315-49789333 chr13:49789318-49789331
50	ELF1	chr13:49789089-49789559	HepG2	liver:	n/a	chr13:49789364-49789373

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49778880..49780737-chr13:49787050..49789935,2	K562	blood:
2	chr13:49787233..49790082-chr13:49795367..49797437,2	MCF-7	breast:

Variant related genes	Relation type
OGFOD1P1	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1013347	0.81[AMR][1000 genomes]
rs1359066	0.95[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs1407827	0.95[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs1407829	0.95[CEU][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs1535922	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1928109	0.86[CEU][hapmap]
rs1937181	1.00[CEU][hapmap]
rs1983805	0.95[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs2026029	0.95[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs2075610	0.86[CHD][hapmap];0.91[GIH][hapmap]
rs2146748	0.94[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap]
rs2147399	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2181539	1.00[CEU][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs2183095	0.91[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs2407266	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs2897633	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs2897689	0.85[CEU][hapmap]
rs2994377	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs2994378	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs2994379	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs2994380	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs3012116	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs3012117	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs3012121	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs3012127	1.00[CEU][hapmap]
rs35018425	0.91[EUR][1000 genomes]
rs4142065	0.95[CEU][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs4245350	0.91[EUR][1000 genomes]
rs4530025	0.94[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap]
rs4942799	0.95[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs4942800	0.95[CEU][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap]
rs6561496	1.00[CEU][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs6561497	0.80[CHD][hapmap];0.98[GIH][hapmap]
rs6561504	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs67235936	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7139746	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7139819	0.87[EUR][1000 genomes]
rs716722	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7317908	0.91[EUR][1000 genomes]
rs7333097	0.82[CHD][hapmap]
rs7333285	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs7338529	0.95[CEU][hapmap];0.80[JPT][hapmap]
rs7983885	0.95[CEU][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs7986624	0.86[CEU][hapmap]
rs7987258	0.87[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs7988168	1.00[CEU][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs7989175	0.80[CHD][hapmap]
rs7990573	0.80[AMR][1000 genomes]
rs7994845	0.90[EUR][1000 genomes]
rs7994910	0.95[CEU][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs7995616	0.95[CEU][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs7996151	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9316428	1.00[CEU][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs9526518	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs9526521	0.98[GIH][hapmap]
rs9526525	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9526532	0.84[GIH][hapmap];0.80[AMR][1000 genomes]
rs9535136	1.00[CEU][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs9535145	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs9535146	1.00[CEU][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs9535147	0.95[CEU][hapmap]
rs9535149	1.00[CEU][hapmap]
rs9535154	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs9535155	1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9535156	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs9535166	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9535167	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9535172	0.82[AMR][1000 genomes]
rs9562866	1.00[CEU][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs9562870	0.95[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs9568150	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs9568151	1.00[CEU][hapmap]
rs9568154	0.81[JPT][hapmap]
rs9568169	0.86[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap]
rs9596064	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv832607	chr13:49756458-49920894	Flanking Bivalent TSS/Enh Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49748800-49790600	Weak transcription	K562	blood
2	chr13:49762800-49789200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:49763400-49789200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr13:49765600-49793800	Weak transcription	A549	lung
5	chr13:49773000-49789600	Weak transcription	NHEK	skin
6	chr13:49773400-49789200	Weak transcription	Brain Angular Gyrus	brain
7	chr13:49774000-49789200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr13:49778000-49793800	Weak transcription	Right Ventricle	heart
9	chr13:49778200-49789200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr13:49778200-49789200	Weak transcription	Esophagus	oesophagus
11	chr13:49781400-49789200	Weak transcription	Primary T cells from cord blood	blood
12	chr13:49781600-49790000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr13:49781600-49790000	Weak transcription	Brain Germinal Matrix	brain
14	chr13:49782000-49789400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr13:49782600-49792600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr13:49782800-49789400	Weak transcription	Adipose Nuclei	Adipose
17	chr13:49782800-49790200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr13:49783000-49789600	Weak transcription	NHDF-Ad	bronchial
19	chr13:49783200-49789600	Weak transcription	HMEC	breast
20	chr13:49783200-49789800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr13:49783400-49789200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr13:49783800-49789600	Weak transcription	HUVEC	blood vessel
23	chr13:49784800-49789600	Weak transcription	NH-A	brain
24	chr13:49785000-49789200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr13:49785200-49789200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr13:49785200-49789600	Weak transcription	Fetal Intestine Large	intestine
27	chr13:49785200-49790600	Weak transcription	Fetal Intestine Small	intestine
28	chr13:49786200-49789200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr13:49786400-49789200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr13:49786400-49790800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr13:49786400-49790800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr13:49786600-49791000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr13:49786600-49792600	Weak transcription	Left Ventricle	heart
34	chr13:49787200-49790800	Enhancers	Primary B cells from cord blood	blood
35	chr13:49787200-49791400	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr13:49787400-49789800	Enhancers	Brain Hippocampus Middle	brain
37	chr13:49787400-49791000	Enhancers	Primary B cells from peripheral blood	blood
38	chr13:49787400-49791400	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr13:49787600-49789200	Enhancers	Brain Substantia Nigra	brain
40	chr13:49787600-49791000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr13:49787800-49789200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr13:49787800-49789800	Enhancers	Hela-S3	cervix
43	chr13:49788000-49789600	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr13:49788000-49789600	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr13:49788000-49791000	Enhancers	Primary hematopoietic stem cells	blood
46	chr13:49788000-49791000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr13:49788200-49789400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr13:49788200-49789400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr13:49788200-49789800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr13:49788400-49789400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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