Variant report

Variant	rs16948722
Chromosome Location	chr17:45920508-45920509
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:186)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:186 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr17:45920383-45920798	HepG2	liver:	n/a	n/a
2	CTCF	chr17:45920449-45920716	Kidney_OC	kidney:	n/a	n/a
3	CHD2	chr17:45920500-45920772	GM12878	blood:	n/a	n/a
4	MYC	chr17:45920508-45920605	GM12878	blood:	n/a	n/a
5	CTCF	chr17:45920314-45921037	MCF-7	breast:	n/a	n/a
6	CTCF	chr17:45920500-45920650	NB4	blood:	n/a	n/a
7	RCOR1	chr17:45920468-45920676	K562	blood:	n/a	n/a
8	CTCF	chr17:45920398-45920808	HepG2	liver:	n/a	n/a
9	CTCF	chr17:45920439-45920743	LNCaP	prostate:	n/a	n/a
10	SMC3	chr17:45920239-45920962	SK-N-SH	brain:	n/a	n/a
11	RAD21	chr17:45920417-45920809	Hela-S3	cervix:	n/a	n/a
12	RAD21	chr17:45920384-45920810	IMR90	lung:	n/a	n/a
13	CTCF	chr17:45920427-45920743	MCF-7	breast:	n/a	n/a
14	CTCF	chr17:45920454-45920721	GM13976	blood:	n/a	n/a
15	SIN3A	chr17:45920415-45920842	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAZ	chr17:45920477-45920765	GM12878	blood:	n/a	n/a
17	HDAC2	chr17:45920423-45920703	K562	blood:	n/a	n/a
18	CTCF	chr17:45920408-45920802	IMR90	lung:	n/a	n/a
19	MAX	chr17:45920458-45920679	K562	blood:	n/a	n/a
20	CTCF	chr17:45920480-45920630	AG04450	lung:	n/a	n/a
21	RAD21	chr17:45920388-45920793	HepG2	liver:	n/a	n/a
22	CTCF	chr17:45920441-45920744	GM13977	blood:	n/a	n/a
23	CTCF	chr17:45920351-45920801	A549	lung:	n/a	n/a
24	RAD21	chr17:45920162-45921079	HCT-116	colon:	n/a	chr17:45921047-45921057
25	CTCF	chr17:45920460-45920610	GM12867	blood:	n/a	n/a
26	YY1	chr17:45920461-45920678	GM12891	blood:	n/a	n/a
27	CTCF	chr17:45920364-45920830	GM12878	blood:	n/a	n/a
28	CTCF	chr17:45920443-45920734	MCF-7	breast:	n/a	n/a
29	CTCF	chr17:45920342-45920849	H1-hESC	embryonic stem cell:	n/a	n/a
30	RCOR1	chr17:45920455-45920725	GM12878	blood:	n/a	n/a
31	FOXM1	chr17:45920308-45920868	GM12878	blood:	n/a	n/a
32	CTCF	chr17:45920500-45920650	HUVEC	blood vessel:	n/a	n/a
33	ZBTB7A	chr17:45920498-45920664	K562	blood:	n/a	n/a
34	CTCF	chr17:45920460-45920610	GM12874	blood:	n/a	n/a
35	EP300	chr17:45920480-45920736	K562	blood:	n/a	chr17:45920684-45920698 chr17:45920676-45920690
36	SMC3	chr17:45920402-45920802	GM12878	blood:	n/a	n/a
37	CTCF	chr17:45920500-45920650	HMF	breast:	n/a	n/a
38	CTCF	chr17:45920474-45920712	HUVEC	blood vessel:	n/a	n/a
39	CTCF	chr17:45920421-45920756	GM12892	blood:	n/a	n/a
40	MXI1	chr17:45920405-45920722	GM12878	blood:	n/a	n/a
41	MAFK	chr17:45920477-45920704	K562	blood:	n/a	n/a
42	CTCF	chr17:45920500-45920650	K562	blood:	n/a	n/a
43	CTCF	chr17:45920437-45920734	A549	lung:	n/a	n/a
44	CTCF	chr17:45920455-45920774	SK-N-SH_RA	brain:	n/a	n/a
45	CTCF	chr17:45920457-45920728	HepG2	liver:	n/a	n/a
46	CTCF	chr17:45920500-45920650	HVMF	connective:	n/a	n/a
47	RAD21	chr17:45920399-45920808	H1-hESC	embryonic stem cell:	n/a	n/a
48	USF2	chr17:45920465-45920522	Hela-S3	cervix:	n/a	n/a
49	RAD21	chr17:45920391-45920812	GM12878	blood:	n/a	n/a
50	MYC	chr17:45920434-45920733	K562	blood:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45919624..45921396-chr17:45944468..45946269,2	K562	blood:
2	chr17:45920145..45920704-chr17:46095754..46096343,3	MCF-7	breast:
3	chr17:45920176..45925286-chr17:46018429..46022644,7	MCF-7	breast:
4	chr17:45920268..45920780-chr17:46025947..46026606,2	MCF-7	breast:
5	chr17:45920242..45924382-chr17:45959879..45966158,9	MCF-7	breast:
6	chr17:45919558..45921234-chr17:45966853..45967975,40	MCF-7	breast:
7	chr17:45920063..45920877-chr17:46026748..46027498,2	K562	blood:
8	chr17:45918850..45921918-chr17:45964837..45968341,4	K562	blood:
9	chr17:45918236..45922252-chr17:45971224..45975227,6	K562	blood:
10	chr17:45919921..45922804-chr17:45938176..45940805,2	MCF-7	breast:
11	chr17:45919993..45920645-chr17:46024002..46024636,2	MCF-7	breast:
12	chr17:45918878..45920635-chr17:45927299..45929830,2	MCF-7	breast:
13	chr17:45919994..45921118-chr17:45966943..45968909,17	K562	blood:
14	chr17:45918706..45921396-chr17:45943154..45946269,3	K562	blood:
15	chr17:45915230..45925590-chr17:45966201..45976437,35	MCF-7	breast:
16	chr17:45919859..45920596-chr17:46095215..46095744,2	MCF-7	breast:
17	chr17:45906340..45909429-chr17:45918735..45922764,3	K562	blood:
18	chr17:45920139..45920699-chr17:46090798..46091462,2	K562	blood:
19	chr17:45919839..45921158-chr17:45966971..45968605,11	MCF-7	breast:
20	chr17:45920026..45921157-chr17:46095429..46096394,5	K562	blood:
21	chr17:45914114..45922201-chr17:45959661..45964608,11	MCF-7	breast:
22	chr17:45920330..45920951-chr17:46023036..46023982,2	MCF-7	breast:
23	chr17:45917897..45920844-chr17:46033567..46035986,3	MCF-7	breast:
24	chr17:45913484..45922782-chr17:45969196..45975741,24	MCF-7	breast:

No data

Variant related genes	Relation type
SCRN2	TF binding region
ENSG00000189120	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000264243	Chromatin interaction
ENSG00000159111	Chromatin interaction
ENSG00000266821	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000141294	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000167182	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1005655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs11079795	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11079796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11650289	0.96[CHB][hapmap];0.91[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11650536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11652439	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11869958	0.95[CHB][hapmap]
rs11870002	0.95[CHB][hapmap]
rs16948401	0.92[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16948590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1985407	0.89[CHB][hapmap]
rs2001380	0.82[EUR][1000 genomes]
rs2001381	0.82[EUR][1000 genomes]
rs2074188	0.96[CHB][hapmap]
rs2074189	0.95[CHB][hapmap]
rs3809869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4794203	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs701984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72833426	0.87[ASN][1000 genomes]
rs8075360	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs878171	0.86[CHB][hapmap]
rs9674817	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv908573	chr17:45858487-45956073	Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv908574	chr17:45876022-45930584	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS 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 miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv517880	chr17:45887951-45933341	Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16948722	OSBPL7	cis	Thyroid	GTEx
rs16948722	SCRN2	Cis_1M	lymphoblastoid	RTeQTL
rs16948722	SCRN2	cis	Whole Blood	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45918600-45922600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:45918800-45920600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr17:45918800-45921000	Enhancers	Rectal Mucosa Donor 29	rectum
4	chr17:45918800-45921200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr17:45918800-45921200	Enhancers	Colonic Mucosa	Colon
6	chr17:45918800-45921200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr17:45918800-45922400	Enhancers	Fetal Intestine Large	intestine
8	chr17:45918800-45924600	Weak transcription	Spleen	Spleen
9	chr17:45919000-45920600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr17:45919000-45920600	Weak transcription	Osteobl	bone
11	chr17:45919000-45920800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr17:45919000-45920800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr17:45919000-45920800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr17:45919000-45920800	Enhancers	Fetal Stomach	stomach
15	chr17:45919000-45921000	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr17:45919000-45921000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr17:45919000-45921000	Enhancers	A549	lung
18	chr17:45919000-45921200	Flanking Active TSS	HepG2	liver
19	chr17:45919000-45921600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr17:45919000-45921800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr17:45919000-45921800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr17:45919000-45922000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr17:45919000-45922200	Enhancers	Fetal Intestine Small	intestine
24	chr17:45919200-45920600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr17:45919200-45920600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr17:45919200-45920600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr17:45919200-45920600	Weak transcription	Fetal Heart	heart
28	chr17:45919200-45920600	Enhancers	Dnd41	blood
29	chr17:45919200-45920800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr17:45919200-45920800	Weak transcription	Esophagus	oesophagus
31	chr17:45919200-45921600	Weak transcription	Right Ventricle	heart
32	chr17:45919200-45921800	Weak transcription	Lung	lung
33	chr17:45919200-45928000	Weak transcription	Right Atrium	heart
34	chr17:45919400-45920600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr17:45919400-45920600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr17:45919400-45920600	Weak transcription	Fetal Muscle Leg	muscle
37	chr17:45919400-45920600	Weak transcription	Small Intestine	intestine
38	chr17:45919400-45920800	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr17:45919400-45921200	Enhancers	GM12878-XiMat	blood
40	chr17:45919400-45922000	Enhancers	Stomach Mucosa	stomach
41	chr17:45919600-45920600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr17:45919600-45920600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr17:45919600-45920600	Enhancers	Liver	Liver
44	chr17:45919800-45922000	Enhancers	Duodenum Mucosa	Duodenum
45	chr17:45920000-45921200	Enhancers	NHEK	skin
46	chr17:45920200-45920600	Enhancers	Brain Anterior Caudate	brain
47	chr17:45920200-45920600	Enhancers	Fetal Kidney	kidney
48	chr17:45920200-45921000	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr17:45920200-45921200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr17:45920200-45921400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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