Variant report

Variant	rs1559709
Chromosome Location	chr4:143483455-143483456
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143475822..143478119-chr4:143482410..143485244,3	MCF-7	breast:
2	chr4:143478683..143482173-chr4:143482213..143486011,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10519649	0.82[GIH][hapmap];0.80[MEX][hapmap]
rs11100748	0.81[ASN][1000 genomes]
rs11939291	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11943687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504375	0.81[ASN][1000 genomes]
rs12505079	0.82[ASN][1000 genomes]
rs12645394	0.88[ASN][1000 genomes]
rs13144094	0.82[ASN][1000 genomes]
rs1425518	0.91[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1476122	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16998558	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16998560	0.83[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs17016344	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17016354	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17016379	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1963849	0.95[ASN][1000 genomes]
rs2042643	0.82[ASN][1000 genomes]
rs2217016	0.91[CEU][hapmap];0.92[CHB][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34223306	0.93[ASN][1000 genomes]
rs4246729	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975306	0.82[GIH][hapmap]
rs4975312	0.94[ASN][1000 genomes]
rs4975313	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975317	0.81[ASN][1000 genomes]
rs57201046	0.95[ASN][1000 genomes]
rs57260347	0.95[ASN][1000 genomes]
rs58078405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58899027	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59732892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60257926	0.87[ASN][1000 genomes]
rs60951295	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61142249	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6537109	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6537110	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67311549	0.95[ASN][1000 genomes]
rs67900719	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814775	0.95[ASN][1000 genomes]
rs6816875	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7664281	0.82[ASN][1000 genomes]
rs7671198	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs890191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs890192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143472600-143486800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:143475600-143488000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:143477800-143484400	Weak transcription	HMEC	breast
4	chr4:143477800-143487000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:143478000-143486600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:143478000-143486800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:143478200-143486000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:143478800-143483600	Weak transcription	Fetal Thymus	thymus
9	chr4:143478800-143488000	Weak transcription	Fetal Intestine Large	intestine
10	chr4:143479200-143487600	Weak transcription	Fetal Intestine Small	intestine
11	chr4:143479200-143488400	Weak transcription	Pancreas	Pancrea
12	chr4:143480200-143485000	Weak transcription	HSMM	muscle
13	chr4:143480200-143487000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:143480400-143484800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:143480600-143487800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:143481200-143486000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr4:143481400-143486000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:143481400-143488400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:143481600-143488400	Weak transcription	Fetal Lung	lung
20	chr4:143481600-143488600	Weak transcription	Osteobl	bone
21	chr4:143481800-143484800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr4:143482000-143483600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr4:143482000-143484800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:143482000-143485000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:143482800-143484200	Strong transcription	Fetal Heart	heart
26	chr4:143482800-143486200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr4:143482800-143486800	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr4:143483000-143486400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:143483200-143484800	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr4:143483200-143485600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:143483200-143486600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr4:143483200-143486800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:143483400-143485200	Enhancers	Thymus	Thymus
34	chr4:143483400-143486200	Enhancers	Primary T killer memory cells from peripheral blood	blood

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