Variant report

Variant	rs16998560
Chromosome Location	chr4:143481466-143481467
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143392466..143394692-chr4:143481340..143483349,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10013367	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10519649	0.88[JPT][hapmap]
rs11100750	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1160379	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11728822	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs11939291	0.83[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs11943687	0.83[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs12505079	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12645394	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13144094	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13145040	0.81[ASN][1000 genomes]
rs1476122	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs1559709	0.83[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs17016354	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs17016379	0.91[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17717651	0.83[JPT][hapmap]
rs1963849	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1974940	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2042643	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2059510	0.87[JPT][hapmap]
rs34007357	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34223306	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4975306	0.88[JPT][hapmap]
rs4975312	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4975314	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57201046	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs57260347	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58078405	0.87[ASN][1000 genomes]
rs59732892	0.87[ASN][1000 genomes]
rs60257926	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60951295	0.87[ASN][1000 genomes]
rs61142249	0.86[ASN][1000 genomes]
rs6537110	0.85[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs67078907	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67311549	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs67900719	0.87[ASN][1000 genomes]
rs6814775	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6826090	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7655599	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7664281	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7694593	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs890191	0.92[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs890192	0.83[CHB][hapmap];0.89[JPT][hapmap];0.87[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:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143471200-143481800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:143471400-143481800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:143472600-143486800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:143475600-143488000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:143477800-143484400	Weak transcription	HMEC	breast
6	chr4:143477800-143487000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:143478000-143486600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:143478000-143486800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:143478200-143486000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:143478400-143482000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:143478800-143482200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr4:143478800-143483600	Weak transcription	Fetal Thymus	thymus
13	chr4:143478800-143488000	Weak transcription	Fetal Intestine Large	intestine
14	chr4:143479200-143487600	Weak transcription	Fetal Intestine Small	intestine
15	chr4:143479200-143488400	Weak transcription	Pancreas	Pancrea
16	chr4:143479800-143482000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:143480000-143482200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:143480200-143481600	Enhancers	Fetal Lung	lung
19	chr4:143480200-143485000	Weak transcription	HSMM	muscle
20	chr4:143480200-143487000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:143480400-143482000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:143480400-143483400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr4:143480400-143484800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:143480600-143482000	Enhancers	Fetal Heart	heart
25	chr4:143480600-143482200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr4:143480600-143487800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr4:143481000-143482000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr4:143481200-143481600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr4:143481200-143481800	Enhancers	Primary T cells fromperipheralblood	blood
30	chr4:143481200-143482000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:143481200-143482000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:143481200-143482000	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr4:143481200-143482000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr4:143481200-143486000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:143481400-143481600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:143481400-143481600	Enhancers	Osteobl	bone
37	chr4:143481400-143481800	Weak transcription	NHLF	lung
38	chr4:143481400-143482600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:143481400-143482800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:143481400-143486000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:143481400-143488400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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