Variant report

Variant	rs58695897
Chromosome Location	chr17:45960948-45960949
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR3C1	chr17:45960610-45961007	A549	lung:	n/a	chr17:45960763-45960789 chr17:45960768-45960784 chr17:45960767-45960785 chr17:45960763-45960789 chr17:45960777-45960786 chr17:45960763-45960789 chr17:45960763-45960789 chr17:45960769-45960783 chr17:45960769-45960783 chr17:45960792-45960806 chr17:45960768-45960784
2	NR3C1	chr17:45960462-45961072	A549	lung:	n/a	chr17:45960763-45960789 chr17:45960768-45960784 chr17:45960767-45960785 chr17:45960763-45960789 chr17:45960777-45960786 chr17:45960763-45960789 chr17:45960763-45960789 chr17:45960769-45960783 chr17:45960769-45960783 chr17:45960792-45960806 chr17:45960768-45960784
3	NR3C1	chr17:45960439-45961056	A549	lung:	n/a	chr17:45960763-45960789 chr17:45960768-45960784 chr17:45960767-45960785 chr17:45960763-45960789 chr17:45960777-45960786 chr17:45960763-45960789 chr17:45960763-45960789 chr17:45960769-45960783 chr17:45960769-45960783 chr17:45960792-45960806 chr17:45960768-45960784
4	REST	chr17:45960868-45961142	ECC-1	luminal epithelium:	n/a	n/a
5	NR3C1	chr17:45960570-45960969	A549	lung:	n/a	chr17:45960763-45960789 chr17:45960768-45960784 chr17:45960767-45960785 chr17:45960763-45960789 chr17:45960777-45960786 chr17:45960763-45960789 chr17:45960763-45960789 chr17:45960769-45960783 chr17:45960769-45960783 chr17:45960792-45960806 chr17:45960768-45960784

No.	Distal block	Cell Line	Cell type
1	chr17:45960153..45962161-chr17:45965804..45967901,2	K562	blood:
2	chr17:45958143..45959731-chr17:45960109..45961631,2	MCF-7	breast:
3	chr17:45928046..45933138-chr17:45958246..45966286,8	K562	blood:
4	chr17:45907055..45909766-chr17:45960466..45962519,2	K562	blood:
5	chr17:45959646..45962824-chr17:45972724..45975938,3	K562	blood:
6	chr17:45907369..45910442-chr17:45960677..45964479,4	MCF-7	breast:
7	chr17:45920242..45924382-chr17:45959879..45966158,9	MCF-7	breast:
8	chr17:45952271..45953858-chr17:45960670..45962936,2	MCF-7	breast:
9	chr17:45959646..45961170-chr17:45972984..45974723,2	K562	blood:
10	chr17:45928961..45933138-chr17:45960892..45963467,3	K562	blood:
11	chr17:45960015..45962438-chr17:45993771..45995735,2	MCF-7	breast:
12	chr17:45960557..45963296-chr17:46100830..46102768,2	MCF-7	breast:
13	chr17:45960588..45963155-chr17:45965865..45967382,2	MCF-7	breast:
14	chr17:45950457..45952482-chr17:45959947..45962257,2	K562	blood:
15	chr17:45955819..45958170-chr17:45960377..45962855,3	K562	blood:
16	chr17:45959973..45962881-chr17:45970750..45975397,6	MCF-7	breast:
17	chr17:45914114..45922201-chr17:45959661..45964608,11	MCF-7	breast:
18	chr17:45949537..45952014-chr17:45960659..45962461,3	MCF-7	breast:
19	chr17:45954484..45959209-chr17:45960047..45963266,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266821	TF binding region
ENSG00000189120	Chromatin interaction
ENSG00000159111	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000141294	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	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12232488	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12453773	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16949270	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16949296	0.92[EUR][1000 genomes]
rs3764393	0.97[EUR][1000 genomes]
rs4450442	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4614773	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006220	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56124407	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56218899	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61702159	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213084	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7214154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217147	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219107	0.97[ASN][1000 genomes]
rs8082055	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9944405	1.00[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:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45954600-45964400	Enhancers	Fetal Intestine Large	intestine
2	chr17:45956400-45961600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:45956400-45961800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr17:45956400-45962400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr17:45956600-45961200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr17:45956600-45961800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr17:45956600-45961800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:45956600-45962000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr17:45956800-45961800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr17:45957600-45964200	Enhancers	Fetal Intestine Small	intestine
11	chr17:45958000-45962200	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr17:45958200-45964400	Enhancers	Placenta	Placenta
13	chr17:45958400-45963000	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr17:45958600-45961800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:45959000-45961400	Enhancers	Lung	lung
16	chr17:45959000-45963600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
17	chr17:45959200-45961000	Enhancers	Right Ventricle	heart
18	chr17:45959200-45961200	Enhancers	Spleen	Spleen
19	chr17:45959200-45963800	Enhancers	Fetal Thymus	thymus
20	chr17:45959400-45962200	Enhancers	Fetal Kidney	kidney
21	chr17:45959400-45963400	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr17:45959600-45961000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr17:45959600-45961000	Enhancers	Esophagus	oesophagus
24	chr17:45959600-45962400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr17:45959600-45962600	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr17:45959600-45963000	Enhancers	Fetal Lung	lung
27	chr17:45959600-45963200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
28	chr17:45959600-45963600	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr17:45959600-45963600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr17:45959800-45961000	Enhancers	Right Atrium	heart
31	chr17:45959800-45962600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr17:45959800-45963200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr17:45959800-45963400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr17:45959800-45963400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr17:45960000-45962400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr17:45960000-45962800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr17:45960000-45963200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr17:45960000-45963200	Enhancers	Stomach Mucosa	stomach
39	chr17:45960000-45971800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr17:45960000-45972200	Weak transcription	HUVEC	blood vessel
41	chr17:45960200-45961000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr17:45960200-45961200	Enhancers	Left Ventricle	heart
43	chr17:45960200-45961800	Weak transcription	NHEK	skin
44	chr17:45960200-45962000	Enhancers	Adipose Nuclei	Adipose
45	chr17:45960200-45962200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr17:45960200-45962400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr17:45960200-45962600	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr17:45960200-45962600	Weak transcription	HMEC	breast
49	chr17:45960200-45963400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr17:45960200-45963600	Enhancers	Primary T cells from cord blood	blood

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