Variant report

Variant	rs702742
Chromosome Location	chr5:154209024-154209025
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:154208960-154209070	MCF-7	breast:	n/a	n/a
2	MYC	chr5:154208771-154209850	MCF10A-Er-Src	breast:	n/a	n/a
3	GATA3	chr5:154209004-154210075	MCF-7	breast:	n/a	n/a
4	STAT3	chr5:154208922-154209963	MCF10A-Er-Src	breast:	n/a	n/a
5	CTCF	chr5:154208952-154209079	MCF-7	breast:	n/a	n/a
6	CTCF	chr5:154208940-154209090	MCF-7	breast:	n/a	n/a
7	RCOR1	chr5:154208886-154209218	K562	blood:	n/a	n/a
8	CTCF	chr5:154208980-154209130	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:154208816-154209475	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr5:154208861-154209182	HepG2	liver:	n/a	n/a
11	RAD21	chr5:154208832-154209183	HepG2	liver:	n/a	n/a
12	TCF12	chr5:154209004-154210012	MCF-7	breast:	n/a	chr5:154209623-154209630
13	JUND	chr5:154208927-154210227	HCT-116	colon:	n/a	n/a
14	POLR2A	chr5:154209017-154209092	K562	blood:	n/a	n/a
15	CTCF	chr5:154208868-154209122	K562	blood:	n/a	n/a
16	POLR2A	chr5:154208631-154209775	SK-N-MC	brain:	n/a	n/a
17	RAD21	chr5:154208768-154209318	MCF-7	breast:	n/a	n/a
18	E2F4	chr5:154208936-154209414	MCF10A-Er-Src	breast:	n/a	n/a
19	RAD21	chr5:154208868-154209135	SK-N-SH_RA	brain:	n/a	n/a
20	SIN3AK20	chr5:154208578-154210128	MCF-7	breast:	n/a	n/a
21	FOSL1	chr5:154208908-154210102	HCT-116	colon:	n/a	n/a
22	GATA3	chr5:154208702-154210005	MCF-7	breast:	n/a	chr5:154208978-154208988
23	CTCF	chr5:154208922-154209091	MCF-7	breast:	n/a	n/a
24	MAX	chr5:154208637-154209924	MCF-7	breast:	n/a	n/a
25	POLR2A	chr5:154208837-154209108	H1-hESC	embryonic stem cell:	n/a	n/a
26	JUND	chr5:154208942-154210058	HCT-116	colon:	n/a	n/a
27	CTCF	chr5:154208954-154209082	MCF-7	breast:	n/a	n/a
28	POLR2A	chr5:154208791-154209557	K562	blood:	n/a	n/a
29	RAD21	chr5:154208883-154209150	HepG2	liver:	n/a	n/a
30	POLR2A	chr5:154208874-154209594	HepG2	liver:	n/a	n/a
31	CTCF	chr5:154208880-154209030	HepG2	liver:	n/a	n/a
32	FOS	chr5:154208763-154210508	MCF10A-Er-Src	breast:	n/a	n/a
33	CTCF	chr5:154208896-154209102	HepG2	liver:	n/a	n/a
34	SP1	chr5:154208774-154210165	HCT-116	colon:	n/a	n/a
35	RAD21	chr5:154208721-154209271	MCF-7	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:154206588..154209257-chr5:154235210..154237943,2	K562	blood:
2	chr5:154205913..154219158-chr5:154234172..154242635,38	MCF-7	breast:
3	chr5:154207634..154212086-chr5:154212438..154216728,14	MCF-7	breast:
4	chr5:154133318..154137368-chr5:154208082..154212477,8	MCF-7	breast:
5	chr5:154200501..154205115-chr5:154206575..154209973,5	MCF-7	breast:

No data

Variant related genes	Relation type
FAXDC2	TF binding region
ENSG00000170271	Chromatin interaction
ENSG00000155508	Chromatin interaction
ENSG00000155506	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1035368	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10515727	1.00[TSI][hapmap]
rs11167705	0.84[ASN][1000 genomes]
rs12187921	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs12188498	1.00[TSI][hapmap]
rs12188828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12300	0.87[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1421815	1.00[TSI][hapmap]
rs1421819	1.00[TSI][hapmap]
rs164195	0.85[EUR][1000 genomes]
rs17096232	1.00[TSI][hapmap]
rs17116409	1.00[TSI][hapmap]
rs17116411	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17116414	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17116417	1.00[TSI][hapmap]
rs17116421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17116433	1.00[CHB][hapmap]
rs17116442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116534	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs180846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs186971	0.89[EUR][1000 genomes]
rs1974776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1974777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2042168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2112223	1.00[CEU][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes]
rs2161128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2258437	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2396999	0.93[CEU][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes]
rs2431184	0.92[ASN][1000 genomes]
rs2544859	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs2544860	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2544866	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2544874	0.97[EUR][1000 genomes]
rs2544875	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2544876	0.97[EUR][1000 genomes]
rs2544880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2544884	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs255529	0.86[ASN][1000 genomes]
rs2560063	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2644743	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2644744	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2644746	0.92[EUR][1000 genomes]
rs2688186	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688187	0.97[EUR][1000 genomes]
rs2688188	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688189	0.97[EUR][1000 genomes]
rs2688190	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2688191	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688193	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688194	0.83[EUR][1000 genomes]
rs2688195	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2688198	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2688199	0.95[EUR][1000 genomes]
rs2688200	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688206	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2688208	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs32427	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs348739	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs348748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs348749	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs348750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs348751	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs348752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs348754	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3776984	1.00[TSI][hapmap]
rs39614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4354100	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs454161	0.92[ASN][1000 genomes]
rs4958771	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55770418	0.92[EUR][1000 genomes]
rs56374414	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58415346	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59525998	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59749917	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580122	0.82[ASN][1000 genomes]
rs6865950	1.00[TSI][hapmap]
rs6879277	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6884416	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895741	1.00[TSI][hapmap]
rs73276742	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73280705	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7716019	1.00[TSI][hapmap]
rs7723269	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7728194	0.84[EUR][1000 genomes]
rs816717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816718	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs816722	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816734	0.88[ASN][1000 genomes]
rs816743	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs816747	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs888694	0.85[EUR][1000 genomes]
rs960499	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9942412	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]

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	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs702742	EBF1	cis	parietal	SCAN
rs702742	CCDC69	cis	parietal	SCAN
rs702742	ANXA6	cis	parietal	SCAN
rs702742	POMZP3	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154174000-154212200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:154181000-154211600	Strong transcription	Brain Hippocampus Middle	brain
3	chr5:154182000-154211400	Strong transcription	Left Ventricle	heart
4	chr5:154187000-154211400	Strong transcription	Fetal Stomach	stomach
5	chr5:154191800-154211600	Strong transcription	Adipose Nuclei	Adipose
6	chr5:154193000-154211800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:154194000-154209400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:154195600-154214400	Weak transcription	Small Intestine	intestine
9	chr5:154196000-154229200	Weak transcription	Psoas Muscle	Psoas
10	chr5:154196400-154214000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:154197600-154214400	Weak transcription	HUVEC	blood vessel
12	chr5:154197800-154214400	Weak transcription	Hela-S3	cervix
13	chr5:154198600-154211200	Strong transcription	Stomach Smooth Muscle	stomach
14	chr5:154198600-154211400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:154199400-154214400	Weak transcription	Right Atrium	heart
16	chr5:154200200-154209200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr5:154200200-154214400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:154200800-154214000	Weak transcription	Fetal Heart	heart
19	chr5:154201000-154228000	Weak transcription	Fetal Brain Male	brain
20	chr5:154203400-154229000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:154203600-154214400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr5:154203800-154210600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:154203800-154211400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:154204000-154209200	Weak transcription	NHLF	lung
25	chr5:154204000-154210000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:154204200-154209200	Weak transcription	Gastric	stomach
27	chr5:154204200-154209600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr5:154204200-154211000	Weak transcription	Thymus	Thymus
29	chr5:154204200-154214400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr5:154204400-154210000	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr5:154204400-154211400	Strong transcription	Liver	Liver
32	chr5:154204400-154213800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr5:154204400-154213800	Weak transcription	NHDF-Ad	bronchial
34	chr5:154204400-154214400	Weak transcription	Brain Germinal Matrix	brain
35	chr5:154205400-154211400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:154205800-154209800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr5:154205800-154211400	Strong transcription	Fetal Intestine Small	intestine
38	chr5:154206200-154209400	Enhancers	NHEK	skin
39	chr5:154206400-154209200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:154206400-154212800	Strong transcription	Brain Anterior Caudate	brain
41	chr5:154206600-154210600	Enhancers	Primary T cells fromperipheralblood	blood
42	chr5:154206600-154210800	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr5:154206600-154211800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:154206800-154209200	Enhancers	Primary T cells from cord blood	blood
45	chr5:154206800-154209200	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr5:154206800-154209400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:154206800-154210400	Enhancers	HMEC	breast
48	chr5:154206800-154211000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:154206800-154211000	Strong transcription	Brain Cingulate Gyrus	brain
50	chr5:154206800-154211000	Strong transcription	Fetal Lung	lung

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