Variant report

Variant	rs2802240
Chromosome Location	chr13:30097307-30097308
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	chr13:30097084-30097783	ECC-1	luminal epithelium:	n/a	chr13:30097219-30097235
2	POLR2A	chr13:30097112-30098752	K562	blood:	n/a	n/a
3	POLR2A	chr13:30097058-30098290	Hela-S3	cervix:	n/a	n/a
4	TCF12	chr13:30097080-30097783	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr13:30097156-30097742	ECC-1	luminal epithelium:	n/a	chr13:30097716-30097727 chr13:30097717-30097726
6	MAX	chr13:30097046-30097890	ECC-1	luminal epithelium:	n/a	chr13:30097716-30097727 chr13:30097717-30097726
7	ESR1	chr13:30097212-30097574	ECC-1	luminal epithelium:	n/a	n/a
8	TEAD4	chr13:30097093-30097692	ECC-1	luminal epithelium:	n/a	n/a
9	TCF12	chr13:30097066-30098267	ECC-1	luminal epithelium:	n/a	n/a
10	EP300	chr13:30096936-30099091	ECC-1	luminal epithelium:	n/a	chr13:30098814-30098824 chr13:30098684-30098693 chr13:30098503-30098519 chr13:30096996-30097005
11	ESR1	chr13:30097165-30097543	ECC-1	luminal epithelium:	n/a	n/a
12	NR3C1	chr13:30097207-30097486	ECC-1	luminal epithelium:	n/a	n/a
13	NFIC	chr13:30097036-30097774	ECC-1	luminal epithelium:	n/a	chr13:30097219-30097235
14	FOXM1	chr13:30096990-30097671	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr13:30097160-30097544	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr13:30097146-30097972	K562	blood:	n/a	n/a
17	USF1	chr13:30097066-30097913	ECC-1	luminal epithelium:	n/a	n/a
18	TEAD4	chr13:30097040-30097680	ECC-1	luminal epithelium:	n/a	n/a
19	USF1	chr13:30097001-30097957	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr13:30097204-30098585	HL-60	blood:	n/a	n/a
21	EP300	chr13:30097052-30097725	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr13:30094962-30101147	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30090549..30094073-chr13:30094397..30097497,3	K562	blood:
2	chr13:30085195..30087223-chr13:30096814..30099566,2	MCF-7	breast:

Variant related genes	Relation type
SLC7A1	TF binding region
ENSG00000139514	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1018680	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1124594	1.00[ASN][1000 genomes]
rs12427581	0.89[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs12428751	0.81[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs17073661	0.81[ASN][1000 genomes]
rs17660515	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277452	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2482087	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2482089	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2482090	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2482091	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2482092	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2482093	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2490264	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490265	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2490266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490267	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776952	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776953	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776955	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776956	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776958	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776960	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2776978	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776979	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776980	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776981	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776984	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776985	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776986	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2802243	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2802244	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2802245	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2802246	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2802250	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2989592	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2989593	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2989596	1.00[ASN][1000 genomes]
rs3011620	1.00[EUR][1000 genomes]
rs3011622	1.00[EUR][1000 genomes]
rs3011623	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011624	1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3011625	1.00[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3013640	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3013641	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598281	1.00[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430551	chr13:30061100-30113000	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30071000-30128800	Strong transcription	Dnd41	blood
2	chr13:30082000-30106600	Weak transcription	Fetal Kidney	kidney
3	chr13:30082000-30107600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr13:30082800-30111600	Weak transcription	Stomach Mucosa	stomach
5	chr13:30083200-30107200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr13:30084200-30106000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr13:30084200-30107800	Strong transcription	Esophagus	oesophagus
8	chr13:30084200-30110400	Strong transcription	Fetal Intestine Small	intestine
9	chr13:30084200-30110600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr13:30084200-30112600	Strong transcription	NHEK	skin
11	chr13:30084200-30115800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr13:30084400-30111200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr13:30084600-30098000	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr13:30084600-30112200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr13:30084800-30098400	Strong transcription	Gastric	stomach
16	chr13:30084800-30110400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr13:30084800-30110600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr13:30084800-30111600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr13:30085000-30098600	Strong transcription	Pancreas	Pancrea
20	chr13:30085000-30099000	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr13:30085000-30111600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr13:30085200-30098800	Strong transcription	Duodenum Mucosa	Duodenum
23	chr13:30085200-30099800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr13:30085200-30104200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
25	chr13:30085400-30099800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr13:30085600-30098600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr13:30085600-30098600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr13:30085600-30098600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr13:30085600-30111200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr13:30085600-30111600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr13:30085800-30099400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr13:30085800-30115400	Strong transcription	Primary T cells from cord blood	blood
33	chr13:30086000-30110600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr13:30086000-30111200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr13:30086400-30098600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr13:30086600-30098600	Strong transcription	HepG2	liver
37	chr13:30086600-30104800	Weak transcription	Fetal Brain Male	brain
38	chr13:30086800-30097800	Strong transcription	A549	lung
39	chr13:30086800-30098600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr13:30086800-30098800	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr13:30087000-30099200	Strong transcription	Primary hematopoietic stem cells	blood
42	chr13:30087000-30099600	Strong transcription	Fetal Brain Female	brain
43	chr13:30087000-30110200	Strong transcription	GM12878-XiMat	blood
44	chr13:30087200-30098600	Weak transcription	Fetal Lung	lung
45	chr13:30087200-30099000	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr13:30087400-30099600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr13:30087600-30098000	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr13:30087600-30098400	Strong transcription	Brain Anterior Caudate	brain
49	chr13:30087600-30099000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr13:30088000-30104600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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