Variant report

Variant	rs2597167
Chromosome Location	chr17:46047656-46047657
allele	C/T
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	MAX	chr17:46047601-46049109	NB4	blood:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
2	SP1	chr17:46047640-46049097	HCT-116	colon:	n/a	chr17:46048298-46048312 chr17:46048335-46048347 chr17:46048337-46048346 chr17:46048336-46048346 chr17:46048269-46048290 chr17:46048335-46048347 chr17:46048464-46048473 chr17:46048469-46048478 chr17:46048336-46048345 chr17:46048336-46048346
3	SMC3	chr17:46047522-46050410	SK-N-SH	brain:	n/a	n/a
4	MAX	chr17:46047592-46049187	HepG2	liver:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
5	RCOR1	chr17:46047602-46048930	HepG2	liver:	n/a	n/a
6	MXI1	chr17:46047255-46050557	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr17:46047402-46049199	SK-N-SH	brain:	n/a	chr17:46048168-46048177
8	MAX	chr17:46047616-46049260	A549	lung:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
9	MXI1	chr17:46047494-46049540	IMR90	lung:	n/a	n/a
10	MBD4	chr17:46047586-46049078	HepG2	liver:	n/a	n/a
11	SIN3AK20	chr17:46047317-46049226	MCF-7	breast:	n/a	n/a
12	RAD21	chr17:46047598-46049158	SK-N-SH	brain:	n/a	chr17:46048248-46048258
13	MAX	chr17:46047653-46049233	HepG2	liver:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
14	CTCF	chr17:46047393-46050115	A549	lung:	n/a	chr17:46048168-46048177
15	SIX5	chr17:46047597-46049043	A549	lung:	n/a	n/a
16	TCF12	chr17:46047510-46049280	A549	lung:	n/a	chr17:46048921-46048931 chr17:46048795-46048802
17	MYBL2	chr17:46047599-46049073	HepG2	liver:	n/a	n/a
18	MTA3	chr17:46047451-46049121	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46046297..46048098-chr17:46050701..46053030,2	MCF-7	breast:
2	chr17:46047400..46050259-chr17:46124707..46126731,3	MCF-7	breast:
3	chr17:45932084..45934510-chr17:46047359..46049635,2	K562	blood:
4	chr17:45915738..45918906-chr17:46047433..46049662,3	K562	blood:
5	chr17:46033549..46039001-chr17:46046732..46050276,6	K562	blood:
6	chr17:46017765..46021634-chr17:46045854..46051133,6	MCF-7	breast:
7	chr17:45917404..45919085-chr17:46045221..46048078,2	K562	blood:
8	chr17:45971215..45974947-chr17:46046480..46050487,6	MCF-7	breast:
9	chr17:46031321..46037809-chr17:46043555..46050276,13	K562	blood:
10	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
11	chr17:46047245..46051740-chr17:46053378..46057507,6	MCF-7	breast:
12	chr17:45971907..45976557-chr17:46046916..46050358,7	K562	blood:
13	chr17:46047439..46051573-chr17:46055956..46059590,5	MCF-7	breast:
14	chr17:45971907..45974928-chr17:46046916..46050084,5	K562	blood:
15	chr17:46046859..46048450-chr17:46055513..46058232,2	K562	blood:

Variant related genes	Relation type
CDK5RAP3	TF binding region
ENSG00000263412	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000264019	Chromatin interaction
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2525089	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2525099	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2525100	1.00[CHD][hapmap];0.84[LWK][hapmap];1.00[ASN][1000 genomes]
rs2597176	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2923063	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56947799	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60163848	1.00[ASN][1000 genomes]
rs61521088	1.00[ASN][1000 genomes]
rs73321620	1.00[ASN][1000 genomes]
rs73321625	1.00[ASN][1000 genomes]
rs73321628	1.00[ASN][1000 genomes]
rs73321689	1.00[ASN][1000 genomes]
rs73985431	1.00[ASN][1000 genomes]
rs73985445	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078698	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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

Variant related diseases (count:1)

Disease	PMID	Source
Metabolite levels (Pyroglutamine)	23934736	GWAS catalog

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46036600-46047800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:46037800-46047800	Enhancers	Fetal Intestine Large	intestine
3	chr17:46042800-46047800	Weak transcription	Small Intestine	intestine
4	chr17:46043000-46047800	Enhancers	Pancreas	Pancrea
5	chr17:46043000-46047800	Enhancers	Stomach Mucosa	stomach
6	chr17:46044800-46048000	Enhancers	Placenta	Placenta
7	chr17:46045000-46047800	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr17:46045400-46047800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr17:46045400-46047800	Weak transcription	Lung	lung
10	chr17:46045400-46048400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr17:46045600-46047800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr17:46045800-46047800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr17:46045800-46047800	Weak transcription	Ovary	ovary
14	chr17:46045800-46047800	Weak transcription	HSMMtube	muscle
15	chr17:46045800-46047800	Weak transcription	NH-A	brain
16	chr17:46045800-46047800	Weak transcription	NHDF-Ad	bronchial
17	chr17:46045800-46047800	Weak transcription	NHLF	lung
18	chr17:46047000-46047800	Enhancers	Gastric	stomach
19	chr17:46047000-46049400	Active TSS	Rectal Smooth Muscle	rectum
20	chr17:46047200-46047800	Enhancers	Spleen	Spleen
21	chr17:46047200-46048000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr17:46047200-46048000	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr17:46047200-46048000	Enhancers	Esophagus	oesophagus
24	chr17:46047200-46048000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr17:46047200-46048400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr17:46047400-46047800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:46047400-46047800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr17:46047400-46047800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr17:46047400-46047800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr17:46047400-46047800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr17:46047400-46047800	Enhancers	Fetal Heart	heart
32	chr17:46047400-46047800	Enhancers	Fetal Stomach	stomach
33	chr17:46047400-46047800	Enhancers	Fetal Thymus	thymus
34	chr17:46047400-46047800	Enhancers	Right Ventricle	heart
35	chr17:46047400-46047800	Enhancers	Thymus	Thymus
36	chr17:46047400-46047800	Flanking Active TSS	HepG2	liver
37	chr17:46047400-46047800	Enhancers	HMEC	breast
38	chr17:46047400-46048000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr17:46047400-46048000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr17:46047400-46048000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr17:46047400-46048000	Flanking Active TSS	Fetal Intestine Small	intestine
42	chr17:46047400-46048200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr17:46047400-46048200	Flanking Active TSS	Dnd41	blood
44	chr17:46047400-46048400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr17:46047400-46049200	Active TSS	Fetal Kidney	kidney
46	chr17:46047600-46047800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
47	chr17:46047600-46047800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr17:46047600-46047800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr17:46047600-46047800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
50	chr17:46047600-46047800	Enhancers	HUES6 Cell Line	embryonic stem cell

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