Variant report

Variant	rs17842195
Chromosome Location	chr17:15366228-15366229
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:15353769..15358146-chr17:15361916..15367322,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239704	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1019092	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10432020	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1548679	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1548680	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2108757	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2190914	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2323734	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2875140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2906973	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2906977	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2906978	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2906979	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2906980	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2906981	0.84[ASN][1000 genomes]
rs2906982	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2906983	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2906984	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2906985	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2954759	0.90[JPT][hapmap]
rs2954761	0.90[JPT][hapmap]
rs2954765	0.84[AMR][1000 genomes]
rs2954770	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2954771	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2954772	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2954773	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2954774	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2954775	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2954776	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2954777	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2954778	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2954779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56055931	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs728854	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs729355	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs729356	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs729357	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs887033	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs887034	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv907703	chr17:15199907-15370701	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv949172	chr17:15206970-15416808	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15339600-15367000	Weak transcription	A549	lung
2	chr17:15340600-15366800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr17:15340600-15399600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr17:15341400-15366800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr17:15341400-15366800	Weak transcription	Esophagus	oesophagus
6	chr17:15341400-15368400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr17:15341400-15375800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr17:15348600-15366800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr17:15349400-15368800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:15356800-15378000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr17:15357800-15366400	Weak transcription	Brain Germinal Matrix	brain
12	chr17:15357800-15375800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr17:15359200-15404600	Weak transcription	Primary T cells from cord blood	blood
14	chr17:15359400-15386600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr17:15359600-15383000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr17:15360200-15369600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:15360800-15367000	Weak transcription	Spleen	Spleen
18	chr17:15361000-15366400	Weak transcription	Fetal Intestine Large	intestine
19	chr17:15361200-15366400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr17:15361200-15366400	Weak transcription	Right Ventricle	heart
21	chr17:15361200-15387800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr17:15361400-15366400	Weak transcription	Fetal Thymus	thymus
23	chr17:15361400-15366400	Weak transcription	Lung	lung
24	chr17:15361400-15385400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr17:15361600-15366400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr17:15361600-15366400	Weak transcription	HUVEC	blood vessel
27	chr17:15361600-15373200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:15361800-15366400	Weak transcription	Placenta	Placenta
29	chr17:15361800-15367000	Weak transcription	Aorta	Aorta
30	chr17:15361800-15367000	Weak transcription	Small Intestine	intestine
31	chr17:15361800-15369600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr17:15361800-15382000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr17:15362000-15366400	Weak transcription	Psoas Muscle	Psoas
34	chr17:15362000-15368200	Weak transcription	HepG2	liver
35	chr17:15362200-15366400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr17:15362200-15366400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr17:15362200-15366400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr17:15362200-15366400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr17:15362200-15366400	Weak transcription	Left Ventricle	heart
40	chr17:15362200-15366400	Weak transcription	Pancreas	Pancrea
41	chr17:15362200-15366800	Weak transcription	Brain Hippocampus Middle	brain
42	chr17:15362200-15366800	Weak transcription	Brain Substantia Nigra	brain
43	chr17:15362400-15366400	Weak transcription	Fetal Intestine Small	intestine
44	chr17:15362400-15369200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr17:15362600-15366400	Weak transcription	Adipose Nuclei	Adipose
46	chr17:15364000-15366400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr17:15364200-15366400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr17:15365800-15366800	Enhancers	Fetal Stomach	stomach
49	chr17:15365800-15367600	Enhancers	Osteobl	bone
50	chr17:15366000-15366400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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