Variant report

Variant	rs1985407
Chromosome Location	chr17:45897531-45897532
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr17:45897509-45897589	Hela-S3	cervix:	n/a	n/a
2	ZBTB7A	chr17:45897274-45897764	K562	blood:	n/a	n/a
3	NR3C1	chr17:45897412-45898171	A549	lung:	n/a	chr17:45897867-45897880 chr17:45897683-45897696
4	ZNF263	chr17:45897394-45897748	HEK293-T-REx	kidney:	n/a	n/a
5	POLR2A	chr17:45897398-45897815	Hela-S3	cervix:	n/a	n/a
6	ELF1	chr17:45897272-45897696	K562	blood:	n/a	n/a
7	MAZ	chr17:45897371-45897689	K562	blood:	n/a	n/a
8	MAX	chr17:45897291-45897554	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45897420..45900355-chr17:45972655..45975500,3	MCF-7	breast:
2	chr17:45897077..45901616-chr17:45914627..45919028,8	MCF-7	breast:
3	chr17:45895288..45896909-chr17:45896930..45899008,3	MCF-7	breast:
4	chr17:45895199..45899793-chr17:45971655..45976847,6	K562	blood:
5	chr17:45886192..45893448-chr17:45896148..45900071,14	MCF-7	breast:
6	chr17:45894310..45903569-chr17:45906761..45911816,14	MCF-7	breast:

No data

Variant related genes	Relation type
OSBPL7	TF binding region
ENSG00000264920	Chromatin interaction
ENSG00000141294	Chromatin interaction
ENSG00000159111	Chromatin interaction
ENSG00000006025	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000167182	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1005655	0.89[CHB][hapmap]
rs11079795	0.89[CHB][hapmap]
rs11079796	0.89[CHB][hapmap]
rs11650289	0.89[CHB][hapmap]
rs11650536	0.89[CHB][hapmap]
rs11869958	0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs11870002	0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs16948401	0.84[CHB][hapmap]
rs16948590	0.89[CHB][hapmap]
rs16948722	0.89[CHB][hapmap]
rs2023799	0.83[ASN][1000 genomes]
rs2074188	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs2074189	0.94[CHB][hapmap];0.84[JPT][hapmap];0.81[YRI][hapmap];0.88[ASN][1000 genomes]
rs2074191	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs3809869	0.89[CHB][hapmap]
rs6503871	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs701984	0.89[CHB][hapmap]
rs7220419	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs8079715	0.82[ASN][1000 genomes]
rs878171	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9674817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv908572	chr17:45858487-45900856	Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45881600-45897800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr17:45882600-45898600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:45883400-45897600	Strong transcription	Fetal Stomach	stomach
4	chr17:45883400-45898200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr17:45883600-45897800	Weak transcription	Fetal Brain Male	brain
6	chr17:45884000-45898000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:45884000-45898400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr17:45884200-45897600	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr17:45884200-45898200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr17:45884400-45897600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr17:45884800-45898400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr17:45885200-45898000	Weak transcription	Fetal Heart	heart
13	chr17:45887000-45898000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr17:45887000-45898400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr17:45887200-45898200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr17:45887400-45898200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr17:45888400-45897600	Weak transcription	HUVEC	blood vessel
18	chr17:45889600-45898400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr17:45891800-45898200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr17:45892000-45898400	Weak transcription	NHLF	lung
21	chr17:45892600-45898000	Weak transcription	NHEK	skin
22	chr17:45892600-45898200	Weak transcription	Fetal Kidney	kidney
23	chr17:45894000-45898200	Weak transcription	NH-A	brain
24	chr17:45894400-45898200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr17:45894600-45898200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr17:45894600-45898400	Weak transcription	Osteobl	bone
27	chr17:45894800-45897800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr17:45895200-45897600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr17:45895400-45897800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr17:45896000-45897800	Weak transcription	HSMMtube	muscle
31	chr17:45896000-45898200	Weak transcription	Small Intestine	intestine
32	chr17:45896200-45897600	Genic enhancers	Gastric	stomach
33	chr17:45896200-45897800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr17:45896400-45897600	Weak transcription	HepG2	liver
35	chr17:45896400-45898200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr17:45896400-45898200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr17:45896400-45901000	Weak transcription	Aorta	Aorta
38	chr17:45896600-45897800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr17:45896600-45897800	Weak transcription	Liver	Liver
40	chr17:45896600-45898000	Weak transcription	Brain Germinal Matrix	brain
41	chr17:45896600-45898000	Weak transcription	Right Ventricle	heart
42	chr17:45896600-45898400	Weak transcription	Psoas Muscle	Psoas
43	chr17:45896800-45897600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr17:45896800-45897600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr17:45896800-45897600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr17:45896800-45897600	Weak transcription	A549	lung
47	chr17:45896800-45897800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr17:45896800-45897800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr17:45896800-45897800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr17:45896800-45898000	Genic enhancers	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links