Variant report

Variant	rs9676717
Chromosome Location	chr19:39678078-39678079
allele	C/T
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39614775..39617261-chr19:39676809..39678412,2	MCF-7	breast:
2	chr19:39677603..39678128-chr8:72871221..72871723,2	MCF-7	breast:
3	chr19:39676778..39680967-chr19:39681960..39686095,4	K562	blood:
4	chr19:39620772..39621728-chr19:39678018..39679083,4	MCF-7	breast:
5	chr19:39676146..39678266-chr19:39679108..39681372,3	MCF-7	breast:
6	chr19:39612790..39613344-chr19:39677633..39678518,3	MCF-7	breast:
7	chr19:39677174..39681975-chr19:39683439..39687085,6	MCF-7	breast:
8	chr19:39657621..39660070-chr19:39676796..39679772,2	MCF-7	breast:
9	chr19:39677291..39678727-chr19:39818439..39819178,4	K562	blood:
10	chr19:39662169..39664494-chr19:39676603..39678181,2	K562	blood:
11	chr19:39612412..39613536-chr19:39677602..39678408,4	MCF-7	breast:
12	chr19:39047153..39048057-chr19:39677752..39678746,2	K562	blood:
13	chr19:39669910..39671469-chr19:39677971..39680938,2	K562	blood:
14	chr19:39671387..39675690-chr19:39676720..39678693,3	K562	blood:
15	chr19:39624966..39625536-chr19:39678054..39678776,2	MCF-7	breast:
16	chr19:39618887..39621010-chr19:39677122..39680092,2	MCF-7	breast:
17	chr19:39645159..39645930-chr19:39677797..39678451,2	K562	blood:
18	chr19:39656551..39660143-chr19:39675246..39681058,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11668093	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12608805	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12610238	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12985441	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17641276	0.83[CHD][hapmap];0.87[MEX][hapmap]
rs35126134	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9676479	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9676661	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9676717	CNFN	cis	cerebellum	SCAN
rs9676717	PHLDB3	cis	parietal	SCAN
rs9676717	CRX	cis	parietal	SCAN
rs9676717	B9D2	cis	cerebellum	SCAN
rs9676717	B3GNT8	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39657800-39687600	Weak transcription	Right Atrium	heart
2	chr19:39661400-39684600	Weak transcription	HSMM	muscle
3	chr19:39662600-39681800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:39663200-39681400	Weak transcription	Fetal Kidney	kidney
5	chr19:39667400-39679600	Weak transcription	HSMMtube	muscle
6	chr19:39669200-39685800	Weak transcription	NHEK	skin
7	chr19:39669400-39678200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr19:39669600-39678200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr19:39669800-39678200	Weak transcription	Right Ventricle	heart
10	chr19:39670600-39678400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr19:39670800-39678200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:39671000-39678200	Weak transcription	Esophagus	oesophagus
13	chr19:39671000-39678400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr19:39671000-39678400	Weak transcription	Spleen	Spleen
15	chr19:39672000-39683600	Weak transcription	Pancreas	Pancrea
16	chr19:39672400-39678200	Weak transcription	Lung	lung
17	chr19:39672600-39678200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr19:39672600-39678200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:39672800-39678200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr19:39672800-39683600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:39673000-39678200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:39673000-39678200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:39673000-39681400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:39673000-39684200	Weak transcription	Gastric	stomach
25	chr19:39673200-39681400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:39673400-39678200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:39674400-39678200	Weak transcription	A549	lung
28	chr19:39675400-39681800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:39677800-39678200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:39677800-39678200	Enhancers	HepG2	liver
31	chr19:39677800-39678400	Enhancers	Fetal Intestine Large	intestine
32	chr19:39677800-39678400	Enhancers	Placenta	Placenta
33	chr19:39677800-39678400	Bivalent Enhancer	Stomach Mucosa	stomach

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