Variant report

Variant	rs12232488
Chromosome Location	chr17:45970144-45970145
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45961070..45963855-chr17:45969315..45972508,3	MCF-7	breast:
2	chr17:45944883..45946724-chr17:45969960..45972616,2	MCF-7	breast:
3	chr17:45914909..45922277-chr17:45964526..45971003,16	K562	blood:
4	chr17:45927379..45930798-chr17:45968870..45970939,3	MCF-7	breast:
5	chr17:45915230..45925590-chr17:45966201..45976437,35	MCF-7	breast:
6	chr17:45969751..45975935-chr17:46032072..46038613,14	MCF-7	breast:
7	chr17:45907261..45910696-chr17:45969933..45974046,5	MCF-7	breast:
8	chr17:45913484..45922782-chr17:45969196..45975741,24	MCF-7	breast:
9	chr17:45881168..45883142-chr17:45967406..45970372,2	MCF-7	breast:
10	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SP6-2	chr17:45969220-45973158	ENSG00000264920.1

No data

Variant related genes	Relation type
ENSG00000264019	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000141294	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000263798	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000159111	Chromatin interaction
ENSG00000167183	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1133221	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12453773	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16949270	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16949296	0.94[EUR][1000 genomes]
rs3764393	0.98[EUR][1000 genomes]
rs4450442	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4614773	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56006220	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56124407	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56218899	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58695897	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61702159	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7213084	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7214154	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7217147	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7219107	0.97[ASN][1000 genomes]
rs8082055	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9944405	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45960000-45971800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr17:45960000-45972200	Weak transcription	HUVEC	blood vessel
3	chr17:45960400-45972000	Weak transcription	Colon Smooth Muscle	Colon
4	chr17:45962200-45970800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr17:45962200-45971800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr17:45962600-45971200	Weak transcription	Gastric	stomach
7	chr17:45963000-45971800	Weak transcription	Fetal Lung	lung
8	chr17:45963200-45971400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr17:45963200-45971400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr17:45963400-45971400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr17:45963400-45971800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr17:45963400-45971800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr17:45963400-45971800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr17:45963400-45972000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr17:45963400-45972200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr17:45963400-45972600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr17:45963600-45970800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr17:45963600-45971600	Weak transcription	Fetal Muscle Leg	muscle
19	chr17:45963600-45971800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr17:45963600-45972000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr17:45963600-45972000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr17:45963600-45972200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr17:45963600-45972400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr17:45964200-45971200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr17:45964400-45971800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr17:45964400-45971800	Weak transcription	Fetal Intestine Large	intestine
27	chr17:45964600-45971600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr17:45965800-45971800	Weak transcription	Brain Angular Gyrus	brain
29	chr17:45966000-45972000	Weak transcription	HSMM	muscle
30	chr17:45966400-45971000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr17:45966400-45971800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr17:45966800-45971800	Weak transcription	A549	lung
33	chr17:45967400-45971600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr17:45967400-45971800	Weak transcription	Fetal Intestine Small	intestine
35	chr17:45967400-45972000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr17:45967600-45971400	Weak transcription	Placenta	Placenta
37	chr17:45967600-45971600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr17:45967600-45971600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr17:45967600-45971800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr17:45967600-45971800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr17:45967600-45972000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr17:45967600-45972000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr17:45967800-45971200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr17:45967800-45971200	Weak transcription	K562	blood
45	chr17:45967800-45971400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr17:45967800-45971400	Weak transcription	HepG2	liver
47	chr17:45967800-45971600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr17:45967800-45972200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr17:45967800-45972400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr17:45967800-45972400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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