Variant report

Variant	rs1442140
Chromosome Location	chr4:90816023-90816024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
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	WRNIP1	chr4:90815796-90816735	GM12878	blood:	n/a	n/a
2	MAZ	chr4:90815953-90816656	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:90815569-90817326	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr4:90815635-90816795	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr4:90815752-90816786	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr4:90815736-90816784	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr4:90815806-90816725	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr4:90815743-90816150	HUVEC	blood vessel:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:90815973-90816023	HCT-116	colon:	n/a
2	chr4:90815973-90816023	CMK	blood:	n/a
3	chr4:90815973-90816023	Jurkat	blood:	n/a
4	chr4:90815973-90816023	SAEC	small airway:	n/a
5	chr4:90815973-90816023	GM19239	blood:	n/a
6	chr4:90815973-90816023	A549	lung:	n/a
7	chr4:90815973-90816023	PFSK-1	brain:	n/a
8	chr4:90815973-90816023	AG09319	gingival:	n/a
9	chr4:90815973-90816023	AG10803	skin:	n/a
10	chr4:90815973-90816023	ECC-1	luminal epithelium:	n/a
11	chr4:90815973-90816023	HEEpiC	esophagus:	n/a
12	chr4:90815973-90816023	U87	brain:	n/a
13	chr4:90815973-90816023	HCM	heart:	n/a
14	chr4:90815973-90816023	LNCaP	prostate:	n/a
15	chr4:90815973-90816023	NT2-D1	testis:	n/a
16	chr4:90815973-90816023	HUVEC	blood vessel:	n/a
17	chr4:90815973-90816023	BE2_C	brain:	n/a
18	chr4:90815973-90816023	ovcar-3	ovarian:	n/a
19	chr4:90815973-90816023	HCF	heart:	n/a
20	chr4:90815973-90816023	GM12891	blood:	n/a
21	chr4:90815973-90816023	SK-N-SH	brain:	n/a
22	chr4:90815973-90816023	Caco-2	colon:	n/a
23	chr4:90815973-90816023	NHDF-neo	bronchial:	n/a
24	chr4:90815973-90816023	PrEC	prostate:	n/a
25	chr4:90815973-90816023	MCF-7	breast:	n/a
26	chr4:90815973-90816023	AG04449	skin:	fetal
27	chr4:90815973-90816023	BJ	skin:	n/a
28	chr4:90815973-90816023	HMEC	breast:	n/a
29	chr4:90815973-90816023	GM06990	blood:	n/a
30	chr4:90815973-90816023	H1-hESC	embryonic stem cell:	embryo
31	chr4:90815973-90816023	SK-N-MC	brain:	n/a
32	chr4:90815973-90816023	RPTEC	kidney:	n/a
33	chr4:90815973-90816023	MCF10A-Er-Src	breast:	n/a
34	chr4:90815973-90816023	Hepatocyte	liver:	n/a
35	chr4:90815973-90816023	NHBE	bronchial:	n/a
36	chr4:90815973-90816023	AG04450	lung:	fetal
37	chr4:90815973-90816023	SKMC	muscle:	n/a
38	chr4:90815973-90816023	ProgFib	skin:	n/a
39	chr4:90815973-90816023	T-47D	breast:	n/a
40	chr4:90815973-90816023	K562	blood:	n/a
41	chr4:90815973-90816023	SK-N-SH_RA	brain:	n/a
42	chr4:90815973-90816023	HepG2	liver:	n/a
43	chr4:90815973-90816023	HIPEpiC	eye:	n/a
44	chr4:90815973-90816023	NB4	blood:	n/a
45	chr4:90815973-90816023	NH-A	brain:	n/a
46	chr4:90815973-90816023	HPAEpiC	pulmonary alveolar:	n/a
47	chr4:90815973-90816023	PANC-1	pancreas:	n/a
48	chr4:90815973-90816023	HL-60	blood:	n/a
49	chr4:90815973-90816023	AG09309	skin:	n/a
50	chr4:90815973-90816023	GM12892	blood:	n/a

No data

Variant related genes	Relation type
MMRN1	TF binding region
MMRN1	CpG island

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10001067	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10004413	0.87[EUR][1000 genomes]
rs10005233	0.83[MEX][hapmap]
rs10028246	0.82[EUR][1000 genomes]
rs12331318	0.86[EUR][1000 genomes]
rs1348224	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1372507	0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1372517	0.81[AMR][1000 genomes]
rs1372521	0.82[EUR][1000 genomes]
rs1372522	0.82[EUR][1000 genomes]
rs1442129	0.82[CHD][hapmap]
rs1442134	0.85[CEU][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1442135	0.93[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471483	0.87[MEX][hapmap];0.81[AMR][1000 genomes]
rs1822217	0.80[EUR][1000 genomes]
rs1899389	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011543	0.82[ASN][1000 genomes]
rs2301134	0.84[CEU][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2301135	0.82[EUR][1000 genomes]
rs2736994	0.98[ASN][1000 genomes]
rs28403500	0.87[EUR][1000 genomes]
rs28415623	0.82[EUR][1000 genomes]
rs28507349	0.82[EUR][1000 genomes]
rs28734152	0.86[EUR][1000 genomes]
rs28777703	0.87[EUR][1000 genomes]
rs35424815	0.86[EUR][1000 genomes]
rs3756059	0.81[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3756063	0.81[EUR][1000 genomes]
rs3806789	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58864428	0.82[EUR][1000 genomes]
rs6532192	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6532193	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6532198	0.88[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs6812192	0.85[CEU][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6816736	0.82[EUR][1000 genomes]
rs6817001	0.82[EUR][1000 genomes]
rs6831847	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6839608	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6843084	0.82[EUR][1000 genomes]
rs6848181	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763443	0.93[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656954	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7671549	0.87[EUR][1000 genomes]
rs7672979	0.86[EUR][1000 genomes]
rs7680557	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7680761	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7681154	0.83[EUR][1000 genomes]
rs7681440	0.83[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes]
rs7687945	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7691487	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7698219	0.87[EUR][1000 genomes]
rs894280	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9307077	0.86[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]

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	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	nsv997700	chr4:90791866-90920021	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv830005	chr4:90799398-90963420	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1442140	SNCA	cis	cerebellum	SCAN
rs1442140	MMRN1	cis	multi-tissue	Pritchard
rs1442140	MMRN1	cis	lymphoblastoid	seeQTL
rs1442140	DSPP	cis	cerebellum	SCAN
rs1442140	FAM190A	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90815200-90816400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:90815400-90816600	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr4:90815400-90816600	Flanking Active TSS	HUVEC	blood vessel
4	chr4:90815400-90818200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr4:90815600-90816400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr4:90815600-90816400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr4:90815600-90816800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr4:90815600-90816800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:90815600-90816800	Enhancers	Adipose Nuclei	Adipose
10	chr4:90815600-90817400	Flanking Active TSS	Dnd41	blood
11	chr4:90815600-90817800	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr4:90815600-90817800	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr4:90815800-90816600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr4:90815800-90816600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:90815800-90816600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr4:90815800-90816600	Active TSS	Fetal Stomach	stomach
17	chr4:90815800-90816600	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr4:90815800-90816600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr4:90815800-90816800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr4:90815800-90816800	Flanking Active TSS	Fetal Thymus	thymus
21	chr4:90815800-90816800	Flanking Active TSS	Thymus	Thymus
22	chr4:90815800-90816800	Flanking Active TSS	GM12878-XiMat	blood
23	chr4:90815800-90817400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr4:90815800-90820600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr4:90816000-90816200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr4:90816000-90816200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr4:90816000-90816400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:90816000-90816400	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr4:90816000-90816400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr4:90816000-90816400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr4:90816000-90816400	Active TSS	Duodenum Mucosa	Duodenum
32	chr4:90816000-90816600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:90816000-90816600	Enhancers	Spleen	Spleen
34	chr4:90816000-90816800	Enhancers	Primary T cells fromperipheralblood	blood
35	chr4:90816000-90816800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links