Variant report

Variant	rs7681440
Chromosome Location	chr4:90756550-90756551
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:90756533-90756583	T-47D	breast:	n/a
2	chr4:90756533-90756583	LNCaP	prostate:	n/a
3	chr4:90756533-90756583	ECC-1	luminal epithelium:	n/a
4	chr4:90756533-90756583	HIPEpiC	eye:	n/a
5	chr4:90756533-90756583	GM19239	blood:	n/a
6	chr4:90756533-90756583	NHBE	bronchial:	n/a
7	chr4:90756533-90756583	PrEC	prostate:	n/a
8	chr4:90756533-90756583	HEEpiC	esophagus:	n/a
9	chr4:90756533-90756583	HMEC	breast:	n/a
10	chr4:90756533-90756583	AG10803	skin:	n/a
11	chr4:90756533-90756583	HL-60	blood:	n/a
12	chr4:90756533-90756583	HAEpiC	amniotic membrane:	n/a
13	chr4:90756533-90756583	HUVEC	blood vessel:	n/a
14	chr4:90756533-90756583	H1-hESC	embryonic stem cell:	embryo
15	chr4:90756533-90756583	SK-N-SH	brain:	n/a
16	chr4:90756533-90756583	HPAEpiC	pulmonary alveolar:	n/a
17	chr4:90756533-90756583	Hepatocyte	liver:	n/a
18	chr4:90756533-90756583	GM12878	blood:	n/a
19	chr4:90756533-90756583	MCF-7	breast:	n/a
20	chr4:90756533-90756583	Hela-S3	cervix:	n/a
21	chr4:90756533-90756583	MCF10A-Er-Src	breast:	n/a
22	chr4:90756533-90756583	HRE	kidney:	n/a
23	chr4:90756533-90756583	PANC-1	pancreas:	n/a
24	chr4:90756533-90756583	AG04449	skin:	fetal
25	chr4:90756533-90756583	HCPEpiC	choroid plexus:	n/a
26	chr4:90756533-90756583	AoSMC	blood vessel:	n/a
27	chr4:90756533-90756583	NB4	blood:	n/a
28	chr4:90756533-90756583	ProgFib	skin:	n/a
29	chr4:90756533-90756583	HRPEpiC	eye:	n/a
30	chr4:90756533-90756583	HepG2	liver:	n/a
31	chr4:90756533-90756583	SK-N-MC	brain:	n/a
32	chr4:90756533-90756583	AG04450	lung:	fetal
33	chr4:90756533-90756583	A549	lung:	n/a
34	chr4:90756533-90756583	GM12891	blood:	n/a
35	chr4:90756533-90756583	IMR90	lung:	fetal
36	chr4:90756533-90756583	U87	brain:	n/a
37	chr4:90756533-90756583	AG09319	gingival:	n/a
38	chr4:90756533-90756583	CMK	blood:	n/a
39	chr4:90756533-90756583	PFSK-1	brain:	n/a
40	chr4:90756533-90756583	ovcar-3	ovarian:	n/a
41	chr4:90756533-90756583	NH-A	brain:	n/a
42	chr4:90756533-90756583	SAEC	small airway:	n/a
43	chr4:90756533-90756583	BE2_C	brain:	n/a
44	chr4:90756533-90756583	K562	blood:	n/a
45	chr4:90756533-90756583	HCM	heart:	n/a
46	chr4:90756533-90756583	HEK293	kidney:	embryo
47	chr4:90756533-90756583	NHDF-neo	bronchial:	n/a
48	chr4:90756533-90756583	NT2-D1	testis:	n/a
49	chr4:90756533-90756583	GM06990	blood:	n/a
50	chr4:90756533-90756583	RPTEC	kidney:	n/a

No data

Variant related genes	Relation type
ENSG00000247775	CpG island

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10004413	0.87[EUR][1000 genomes]
rs10005233	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10008964	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10028246	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12331318	0.86[EUR][1000 genomes]
rs1348224	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1372517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372518	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1372519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1372520	1.00[ASN][1000 genomes]
rs1372521	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1372522	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1442135	0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs1442140	0.83[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes]
rs1442144	0.83[ASN][1000 genomes]
rs1442148	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1471483	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][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]
rs1471484	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1811442	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1811443	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1812923	0.81[CEU][hapmap]
rs1822217	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1837891	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.83[ASN][1000 genomes]
rs184810	0.81[ASN][1000 genomes]
rs1899389	0.83[AMR][1000 genomes]
rs2197120	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs2245801	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2301134	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2301135	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2572318	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs2572320	0.83[ASN][1000 genomes]
rs2583962	0.83[ASN][1000 genomes]
rs2583964	0.83[ASN][1000 genomes]
rs2583968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2583972	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2583975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2583978	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2619341	0.83[ASN][1000 genomes]
rs2619347	0.84[ASN][1000 genomes]
rs2619349	0.86[ASN][1000 genomes]
rs2619355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2619356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2619368	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[ASN][1000 genomes]
rs2737002	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2737010	0.82[ASN][1000 genomes]
rs2737011	0.86[ASN][1000 genomes]
rs2737021	0.83[ASN][1000 genomes]
rs2737025	0.83[ASN][1000 genomes]
rs2737028	0.83[ASN][1000 genomes]
rs2737030	0.83[ASN][1000 genomes]
rs28403500	0.87[EUR][1000 genomes]
rs28415623	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28507349	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28734152	0.86[EUR][1000 genomes]
rs28777703	0.87[EUR][1000 genomes]
rs3113355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[ASN][1000 genomes]
rs35424815	0.86[EUR][1000 genomes]
rs356162	0.81[ASN][1000 genomes]
rs356186	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs356188	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs356191	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs356198	0.85[YRI][hapmap]
rs3756059	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756063	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806789	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4293762	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58864428	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6532191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6532192	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6532193	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6816736	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6817001	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6828271	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6831847	0.81[AMR][1000 genomes]
rs6839608	0.83[AMR][1000 genomes]
rs6843084	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs748849	0.83[ASN][1000 genomes]
rs763443	0.83[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes]
rs7671549	0.87[EUR][1000 genomes]
rs7672979	0.86[EUR][1000 genomes]
rs7680557	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7680761	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7681154	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7687945	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7698219	0.87[EUR][1000 genomes]
rs894280	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs920624	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs974711	0.81[CEU][hapmap]
rs990085	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv879536	chr4:90678541-90775212	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7681440	SNCA	cis	cerebellum	SCAN
rs7681440	DSPP	cis	cerebellum	SCAN
rs7681440	FAM190A	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90730200-90757200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:90730800-90757000	Weak transcription	Fetal Stomach	stomach
3	chr4:90738400-90756600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr4:90743400-90756600	Weak transcription	NHEK	skin
5	chr4:90743400-90757400	Weak transcription	Gastric	stomach
6	chr4:90743800-90756600	Weak transcription	Ovary	ovary
7	chr4:90751000-90756600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:90751000-90756600	Weak transcription	Fetal Thymus	thymus
9	chr4:90751000-90757200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:90751200-90756600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr4:90751400-90756600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:90751400-90756600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr4:90751400-90757400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:90751600-90756600	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:90751600-90756800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr4:90752000-90757000	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr4:90752600-90756600	Weak transcription	Fetal Lung	lung
18	chr4:90753400-90756600	Genic enhancers	Dnd41	blood
19	chr4:90753600-90756600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:90753800-90757200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:90755600-90756600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
22	chr4:90755600-90757000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr4:90755600-90757000	Enhancers	Brain Angular Gyrus	brain
24	chr4:90755600-90759800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:90755800-90759600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:90755800-90759600	Active TSS	Fetal Brain Female	brain
27	chr4:90756000-90756600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:90756000-90756600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:90756000-90756600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:90756000-90756600	Weak transcription	Brain Anterior Caudate	brain
31	chr4:90756000-90756600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:90756000-90756800	Enhancers	Brain Cingulate Gyrus	brain
33	chr4:90756000-90757000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:90756200-90756800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:90756200-90757400	Flanking Active TSS	Fetal Brain Male	brain
36	chr4:90756200-90757800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:90756400-90756600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:90756400-90756600	Weak transcription	Brain Substantia Nigra	brain
39	chr4:90756400-90756600	Active TSS	HMEC	breast
40	chr4:90756400-90757400	Enhancers	Primary T cells from cord blood	blood

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