Variant report

Variant	rs16945785
Chromosome Location	chr17:60100678-60100679
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60100669..60105191-chr17:60105675..60110995,6	MCF-7	breast:
2	chr17:60004317..60006428-chr17:60099943..60102128,2	MCF-7	breast:
3	chr17:60099767..60102259-chr17:60130440..60133314,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108506	Chromatin interaction
ENSG00000108510	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10221202	0.94[ASN][1000 genomes]
rs1045196	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10512491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12601229	1.00[AFR][1000 genomes]
rs12601523	1.00[AFR][1000 genomes]
rs12603627	0.82[AFR][1000 genomes]
rs12937188	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16945724	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs16945762	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16945823	0.84[AMR][1000 genomes]
rs2378946	0.82[AFR][1000 genomes]
rs28500646	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4280312	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7224854	0.80[ASN][1000 genomes]
rs72843746	0.82[AFR][1000 genomes]
rs72843758	1.00[AFR][1000 genomes]
rs72843759	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72843762	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72843767	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72843769	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72843770	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs72843771	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs72843772	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72843775	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72843778	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72843782	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72843785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72843788	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72843791	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72843793	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72843797	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72843801	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72845403	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72845404	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72845405	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72845406	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72845408	0.84[AMR][1000 genomes]
rs753765	0.82[AFR][1000 genomes]
rs9910451	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1062816	chr17:60074670-60470465	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	esv2753884	chr17:60077852-60190630	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	esv2755037	chr17:60086508-60386211	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60025400-60107600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:60033000-60128400	Weak transcription	Stomach Mucosa	stomach
3	chr17:60042800-60105200	Weak transcription	Psoas Muscle	Psoas
4	chr17:60050200-60100800	Weak transcription	Small Intestine	intestine
5	chr17:60062400-60106800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr17:60069200-60107600	Weak transcription	Spleen	Spleen
7	chr17:60074600-60123800	Weak transcription	Right Atrium	heart
8	chr17:60075800-60114400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr17:60077200-60136800	Strong transcription	Fetal Thymus	thymus
10	chr17:60081800-60111600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr17:60087000-60102200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr17:60088400-60107600	Weak transcription	Pancreas	Pancrea
13	chr17:60088600-60100800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr17:60088600-60105200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr17:60088600-60105400	Weak transcription	Esophagus	oesophagus
16	chr17:60088600-60106800	Weak transcription	Fetal Heart	heart
17	chr17:60094600-60113200	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr17:60095000-60103800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr17:60095000-60112600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr17:60095000-60113200	Strong transcription	Duodenum Mucosa	Duodenum
21	chr17:60095200-60103800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr17:60095600-60105800	Weak transcription	Brain Angular Gyrus	brain
23	chr17:60095800-60103200	Strong transcription	Fetal Intestine Small	intestine
24	chr17:60095800-60103200	Strong transcription	Fetal Stomach	stomach
25	chr17:60095800-60103800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr17:60095800-60112600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr17:60095800-60113000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr17:60096000-60103400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr17:60096000-60103800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr17:60096000-60105200	Weak transcription	NHLF	lung
31	chr17:60096000-60113000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr17:60096800-60105400	Weak transcription	Fetal Brain Male	brain
33	chr17:60097000-60102800	Weak transcription	NHEK	skin
34	chr17:60097000-60113000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr17:60097000-60113000	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr17:60097400-60100800	Weak transcription	Fetal Brain Female	brain
37	chr17:60098600-60102400	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr17:60098600-60104000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr17:60098600-60111400	Strong transcription	Fetal Lung	lung
40	chr17:60098600-60112400	Strong transcription	Fetal Muscle Leg	muscle
41	chr17:60098600-60114600	Strong transcription	Placenta	Placenta
42	chr17:60098600-60139200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr17:60098800-60101000	Strong transcription	Brain Hippocampus Middle	brain
44	chr17:60098800-60101600	Strong transcription	Rectal Smooth Muscle	rectum
45	chr17:60098800-60101800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr17:60098800-60101800	Strong transcription	Brain Germinal Matrix	brain
47	chr17:60098800-60102400	Strong transcription	Gastric	stomach
48	chr17:60098800-60103200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr17:60098800-60103200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr17:60098800-60103400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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