Variant report

Variant	rs56218899
Chromosome Location	chr17:45967279-45967280
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45919558..45921234-chr17:45966853..45967975,40	MCF-7	breast:
2	chr17:45918170..45919472-chr17:45966923..45968195,16	MCF-7	breast:
3	chr17:45919994..45921118-chr17:45966943..45968909,17	K562	blood:
4	chr17:45960588..45963155-chr17:45965865..45967382,2	MCF-7	breast:
5	chr17:45921348..45922971-chr17:45966998..45967914,11	MCF-7	breast:
6	chr17:45943485..45945965-chr17:45965955..45967991,2	K562	blood:
7	chr17:45919839..45921158-chr17:45966971..45968605,11	MCF-7	breast:
8	chr17:45966461..45968599-chr17:46008809..46010665,2	K562	blood:
9	chr17:45914909..45922277-chr17:45964526..45971003,16	K562	blood:
10	chr17:45960153..45962161-chr17:45965804..45967901,2	K562	blood:
11	chr17:45917983..45919482-chr17:45966657..45967952,11	MCF-7	breast:
12	chr17:45915230..45925590-chr17:45966201..45976437,35	MCF-7	breast:
13	chr17:45921946..45922749-chr17:45967042..45967908,3	K562	blood:
14	chr17:45917943..45920264-chr17:45965958..45968372,4	MCF-7	breast:
15	chr17:45926873..45929813-chr17:45964875..45969048,5	MCF-7	breast:
16	chr17:45918850..45921918-chr17:45964837..45968341,4	K562	blood:
17	chr17:45957419..45959674-chr17:45964404..45967485,3	K562	blood:
18	chr17:45966134..45968885-chr17:46018937..46020700,3	MCF-7	breast:
19	chr17:45917998..45919345-chr17:45966962..45967984,18	K562	blood:

No data

Variant related genes	Relation type
ENSG00000189120	Chromatin interaction
ENSG00000266601	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000108439	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	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12232488	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12453773	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16949270	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16949296	0.91[EUR][1000 genomes]
rs3764393	0.95[EUR][1000 genomes]
rs4450442	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4614773	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006220	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56124407	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58695897	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61702159	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213084	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7214154	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217147	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219107	0.97[ASN][1000 genomes]
rs8082055	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9944405	0.98[EUR][1000 genomes];0.98[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:57 , 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	chr17:45963200-45969200	Weak transcription	Stomach Mucosa	stomach
9	chr17:45963200-45971400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr17:45963200-45971400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr17:45963400-45967600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr17:45963400-45971400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr17:45963400-45971800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr17:45963400-45971800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr17:45963400-45971800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr17:45963400-45972000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr17:45963400-45972200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr17:45963400-45972600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr17:45963600-45967600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr17:45963600-45970800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr17:45963600-45971600	Weak transcription	Fetal Muscle Leg	muscle
22	chr17:45963600-45971800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr17:45963600-45972000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr17:45963600-45972000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr17:45963600-45972200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr17:45963600-45972400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr17:45964200-45971200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr17:45964400-45971800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr17:45964400-45971800	Weak transcription	Fetal Intestine Large	intestine
30	chr17:45964600-45971600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr17:45965400-45967800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr17:45965800-45967800	Enhancers	K562	blood
33	chr17:45965800-45971800	Weak transcription	Brain Angular Gyrus	brain
34	chr17:45966000-45972000	Weak transcription	HSMM	muscle
35	chr17:45966200-45967600	Enhancers	Placenta	Placenta
36	chr17:45966400-45967600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr17:45966400-45967600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr17:45966400-45971000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr17:45966400-45971800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr17:45966800-45971800	Weak transcription	A549	lung
41	chr17:45967200-45967400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr17:45967200-45967400	Enhancers	Brain Cingulate Gyrus	brain
43	chr17:45967200-45967400	Enhancers	Fetal Brain Male	brain
44	chr17:45967200-45967400	Enhancers	Fetal Intestine Small	intestine
45	chr17:45967200-45967400	Enhancers	Stomach Smooth Muscle	stomach
46	chr17:45967200-45967600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr17:45967200-45967600	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr17:45967200-45967600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr17:45967200-45967800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr17:45967200-45967800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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