Variant report

Variant	rs17016354
Chromosome Location	chr4:143472696-143472697
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:143394598..143397673-chr4:143470943..143474173,4	MCF-7	breast:
2	chr4:143448680..143450271-chr4:143471628..143474463,2	MCF-7	breast:
3	chr4:143470903..143473181-chr4:143503452..143506011,2	MCF-7	breast:
4	chr4:143390493..143399629-chr4:143464669..143473703,24	MCF-7	breast:
5	chr4:143470482..143472862-chr4:143765653..143767436,2	MCF-7	breast:
6	chr4:143469197..143474225-chr4:143534708..143538333,6	MCF-7	breast:
7	chr4:143471348..143473653-chr4:143477211..143480066,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10013367	0.84[ASN][1000 genomes]
rs10519649	0.80[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11100748	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11100749	0.83[AMR][1000 genomes]
rs11100750	0.84[ASN][1000 genomes]
rs1160379	0.80[ASN][1000 genomes]
rs11939291	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11943687	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12504375	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12504378	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12504770	0.80[EUR][1000 genomes]
rs12645394	0.82[ASN][1000 genomes]
rs13144094	0.87[ASN][1000 genomes]
rs1425518	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1425519	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1476122	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1559709	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]
rs16998558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16998560	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs17016344	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17016379	0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs17717651	0.83[CHB][hapmap];0.80[EUR][1000 genomes]
rs1963849	0.90[ASN][1000 genomes]
rs1974940	0.84[ASN][1000 genomes]
rs2059510	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2059511	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2059513	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2217016	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34007357	0.80[ASN][1000 genomes]
rs34223306	0.88[ASN][1000 genomes]
rs35854467	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4246729	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4524461	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4975306	0.85[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs4975312	0.89[ASN][1000 genomes]
rs4975313	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975314	0.84[ASN][1000 genomes]
rs4975316	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4975317	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4975318	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57201046	0.90[ASN][1000 genomes]
rs57260347	0.90[ASN][1000 genomes]
rs58078405	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58899027	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59732892	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60257926	0.81[ASN][1000 genomes]
rs60951295	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61104737	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61142249	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6537109	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6537110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67078907	0.84[ASN][1000 genomes]
rs67311549	0.90[ASN][1000 genomes]
rs67900719	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6814775	0.90[ASN][1000 genomes]
rs6816875	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6826090	0.84[ASN][1000 genomes]
rs7655599	0.84[ASN][1000 genomes]
rs7671198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs890191	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs890192	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17016354	C7orf25	trans	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143465600-143472800	Weak transcription	Fetal Lung	lung
2	chr4:143468400-143473400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:143468600-143473200	Enhancers	Fetal Intestine Small	intestine
4	chr4:143468800-143480000	Weak transcription	Left Ventricle	heart
5	chr4:143469000-143473400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:143469400-143477200	Weak transcription	Psoas Muscle	Psoas
7	chr4:143470000-143473200	Enhancers	NH-A	brain
8	chr4:143470200-143472800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:143470200-143473600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:143470200-143474800	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr4:143470200-143477400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr4:143470400-143473200	Enhancers	HSMM	muscle
13	chr4:143470400-143478000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr4:143470600-143473200	Enhancers	Osteobl	bone
15	chr4:143470600-143474200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:143470600-143475000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr4:143470800-143478600	Weak transcription	Pancreas	Pancrea
18	chr4:143471000-143473000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:143471000-143473400	Enhancers	HMEC	breast
20	chr4:143471000-143475600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:143471200-143473600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr4:143471200-143481800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:143471400-143472800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:143471400-143472800	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr4:143471400-143473200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:143471400-143473800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:143471400-143477600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr4:143471400-143477600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr4:143471400-143481800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:143471600-143473200	Enhancers	NHEK	skin
31	chr4:143471600-143476200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:143471600-143480000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:143471800-143474400	Enhancers	A549	lung
34	chr4:143472000-143473600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:143472200-143474000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:143472200-143478600	Weak transcription	Fetal Heart	heart
37	chr4:143472400-143474400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr4:143472400-143481200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:143472600-143474600	Weak transcription	Fetal Intestine Large	intestine
40	chr4:143472600-143477800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:143472600-143486800	Weak transcription	Rectal Mucosa Donor 31	rectum

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