Variant report

Variant	rs17016306
Chromosome Location	chr4:143440396-143440397
allele	C/T
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	PBX3	chr4:143440396-143440942	SK-N-SH	brain:	n/a	n/a
2	RAD21	chr4:143440328-143441076	SK-N-SH	brain:	n/a	n/a
3	JUND	chr4:143440396-143440992	SK-N-SH	brain:	n/a	chr4:143440798-143440809 chr4:143440801-143440810 chr4:143440803-143440810 chr4:143440800-143440811
4	EP300	chr4:143439610-143441148	SK-N-SH	brain:	n/a	chr4:143440560-143440568 chr4:143440801-143440810
5	GATA3	chr4:143440307-143441124	SK-N-SH	brain:	n/a	chr4:143440709-143440725 chr4:143440800-143440809
6	CTCF	chr4:143440377-143441027	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr4:143440377-143441055	SK-N-SH	brain:	n/a	chr4:143440657-143440664
8	PBX3	chr4:143440372-143441068	SK-N-SH	brain:	n/a	n/a
9	CTCF	chr4:143440365-143440993	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:143438526..143441082-chr4:143443050..143445665,2	MCF-7	breast:
2	chr4:143438172..143440969-chr4:143448454..143450355,2	K562	blood:
3	chr4:143391320..143397090-chr4:143436268..143441588,7	MCF-7	breast:
4	chr4:143430690..143432706-chr4:143438410..143440914,2	MCF-7	breast:
5	chr4:143439527..143441800-chr4:143442238..143444041,2	MCF-7	breast:
6	chr4:143389462..143399452-chr4:143428707..143442488,28	MCF-7	breast:

Variant related genes	Relation type
INPP4B	TF binding region
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10011782	1.00[CEU][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs10012476	0.82[JPT][hapmap]
rs12108640	0.91[EUR][1000 genomes]
rs12643136	0.82[JPT][hapmap]
rs12646243	0.82[JPT][hapmap]
rs12649139	0.82[JPT][hapmap]
rs1364926	0.82[JPT][hapmap]
rs1391099	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs1425531	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs1425533	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1425534	0.82[JPT][hapmap]
rs1425535	0.81[JPT][hapmap]
rs1425536	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1425537	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1425538	0.82[JPT][hapmap]
rs1489581	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs17016163	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs17016175	0.92[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs17016207	0.82[JPT][hapmap]
rs17016248	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs17016304	0.84[CHD][hapmap]
rs1817970	0.84[CEU][hapmap]
rs1834391	0.93[EUR][1000 genomes]
rs2113996	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2113997	1.00[CEU][hapmap];0.96[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2322705	0.82[JPT][hapmap]
rs2322795	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2874841	0.94[EUR][1000 genomes]
rs2874865	0.93[EUR][1000 genomes]
rs28822497	0.91[EUR][1000 genomes]
rs3844178	0.94[EUR][1000 genomes]
rs3913163	0.92[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs4345256	0.82[JPT][hapmap]
rs4975308	0.93[EUR][1000 genomes]
rs60924405	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs713071	0.94[EUR][1000 genomes]
rs7668133	0.86[JPT][hapmap]
rs7672965	0.92[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs976564	0.93[EUR][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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv461660	chr4:143437219-143538179	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv595605	chr4:143437219-143538179	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143428800-143453000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:143434000-143440600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:143438600-143440400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr4:143438600-143440600	Weak transcription	HSMM	muscle
5	chr4:143438600-143443600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:143438800-143440600	Weak transcription	NHEK	skin
7	chr4:143438800-143443600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:143438800-143444000	Weak transcription	HMEC	breast
9	chr4:143438800-143462800	Weak transcription	Aorta	Aorta
10	chr4:143439000-143452200	Weak transcription	Fetal Heart	heart
11	chr4:143440000-143440600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:143440000-143440800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:143440200-143440400	Enhancers	Fetal Intestine Large	intestine

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