Variant report

Variant	rs7200935
Chromosome Location	chr16:69564497-69564498
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:69564049..69566185-chr16:69596173..69597747,2	K562	blood:
2	chr16:69362513..69364204-chr16:69563809..69565438,2	K562	blood:
3	chr16:69561937..69564667-chr16:70285129..70286658,2	MCF-7	breast:
4	chr16:69441221..69442807-chr16:69563296..69565834,2	K562	blood:
5	chr16:69524110..69526061-chr16:69563586..69566437,2	K562	blood:
6	chr16:69492037..69494585-chr16:69563234..69566280,3	K562	blood:
7	chr16:69563250..69565350-chr16:69571620..69573342,2	K562	blood:
8	chr16:69561206..69567755-chr16:69595684..69602877,15	K562	blood:
9	chr16:69563695..69566237-chr16:69598351..69600283,2	K562	blood:
10	chr16:69563843..69566440-chr16:69590440..69592219,2	K562	blood:
11	chr16:69440915..69442721-chr16:69563296..69565171,2	K562	blood:
12	chr16:69563142..69566271-chr16:69570461..69572776,3	MCF-7	breast:
13	chr16:69561256..69567897-chr16:69597498..69602280,7	MCF-7	breast:
14	chr16:69562466..69565005-chr16:69568063..69569909,2	MCF-7	breast:
15	chr16:69564473..69570135-chr16:69596661..69601236,6	MCF-7	breast:
16	chr16:69563545..69565092-chr16:69567912..69569578,2	K562	blood:
17	chr16:69560207..69562252-chr16:69564012..69565719,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000132604	Chromatin interaction
ENSG00000213380	Chromatin interaction
ENSG00000223496	Chromatin interaction
ENSG00000223109	Chromatin interaction
ENSG00000102908	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10454066	1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs10500551	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs10852457	0.82[EUR][1000 genomes]
rs10852458	1.00[CEU][hapmap]
rs11075728	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs11075730	0.84[CHD][hapmap];0.82[MEX][hapmap]
rs11639947	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs11641233	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs11642030	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12232410	0.95[CEU][hapmap];0.84[CHD][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap]
rs12447326	0.84[CHD][hapmap];0.82[MEX][hapmap]
rs12595869	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs12596731	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12596823	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs12597243	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12599648	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1437135	1.00[CEU][hapmap];0.82[CHD][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs16958970	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs16959025	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs1800566	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs2161631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2361838	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs3169315	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs3743673	1.00[CEU][hapmap]
rs56256040	0.94[EUR][1000 genomes]
rs60099379	0.88[EUR][1000 genomes]
rs7187653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7194753	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7196943	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7197614	0.80[ASN][1000 genomes]
rs7198242	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs72799376	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs8045705	0.88[EUR][1000 genomes]
rs8046314	1.00[CEU][hapmap]
rs920191	0.82[CHD][hapmap]
rs9788837	1.00[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs9921045	1.00[CEU][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs9929720	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[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	nsv431514	chr16:69428599-69581699	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv906821	chr16:69509506-69576894	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7200935	NRN1L	cis	cerebellum	SCAN
rs7200935	CES8	cis	cerebellum	SCAN
rs7200935	LOC440348	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69562400-69565800	Enhancers	Placenta	Placenta
2	chr16:69563000-69564600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr16:69563200-69564600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr16:69563200-69564800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr16:69563200-69564800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr16:69563200-69565000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr16:69563200-69565200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr16:69563200-69565200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr16:69563200-69565200	Enhancers	HepG2	liver
10	chr16:69563200-69565200	Enhancers	HSMM	muscle
11	chr16:69563200-69565200	Enhancers	NH-A	brain
12	chr16:69563200-69565800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr16:69563200-69566400	Enhancers	NHDF-Ad	bronchial
14	chr16:69563400-69565200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr16:69563400-69565200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr16:69563400-69565200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr16:69563400-69565200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr16:69563400-69566200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr16:69563600-69564800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr16:69563600-69564800	Enhancers	Left Ventricle	heart
21	chr16:69563600-69564800	Enhancers	Lung	lung
22	chr16:69563600-69564800	Enhancers	HUVEC	blood vessel
23	chr16:69563600-69564800	Enhancers	NHLF	lung
24	chr16:69563600-69565000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr16:69563600-69565000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr16:69563600-69565000	Enhancers	Fetal Muscle Leg	muscle
27	chr16:69563600-69565000	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr16:69563600-69565000	Enhancers	Small Intestine	intestine
29	chr16:69563600-69565000	Enhancers	Dnd41	blood
30	chr16:69563600-69565200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr16:69563600-69565200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr16:69563600-69565200	Enhancers	Adipose Nuclei	Adipose
33	chr16:69563600-69565200	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr16:69563600-69565200	Enhancers	Placenta Amnion	Placenta Amnion
35	chr16:69563800-69564600	Weak transcription	Fetal Intestine Large	intestine
36	chr16:69563800-69564600	Weak transcription	Right Atrium	heart
37	chr16:69563800-69564800	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr16:69563800-69565200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr16:69564000-69564600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr16:69564000-69564800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr16:69564000-69566600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr16:69564200-69564600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr16:69564200-69564600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr16:69564200-69564800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr16:69564200-69565000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr16:69564400-69564600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr16:69564400-69564600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
48	chr16:69564400-69564600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr16:69564400-69564600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr16:69564400-69564600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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