Variant report

Variant	rs10206961
Chromosome Location	chr2:85814984-85814985
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:100)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:100 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr2:85814685-85815074	K562	blood:	n/a	n/a
2	GATA2	chr2:85814576-85815060	K562	blood:	n/a	n/a
3	FOXA1	chr2:85814570-85815040	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:85814671-85815067	K562	blood:	n/a	n/a
5	CEBPB	chr2:85814589-85815189	K562	blood:	n/a	chr2:85814677-85814686
6	FOXA1	chr2:85814672-85815075	HepG2	liver:	n/a	n/a
7	JUN	chr2:85814572-85815127	K562	blood:	n/a	n/a
8	CBX3	chr2:85814638-85815014	K562	blood:	n/a	n/a
9	SPI1	chr2:85814699-85815027	GM12891	blood:	n/a	n/a
10	CEBPD	chr2:85814559-85815163	K562	blood:	n/a	n/a
11	MYBL2	chr2:85814539-85815139	HepG2	liver:	n/a	chr2:85815034-85815049
12	NR2F2	chr2:85814556-85816546	K562	blood:	n/a	n/a
13	EP300	chr2:85814606-85815114	K562	blood:	n/a	n/a
14	NFIC	chr2:85814598-85815026	HepG2	liver:	n/a	n/a
15	RXRA	chr2:85814649-85815039	HepG2	liver:	n/a	n/a
16	TCF7L2	chr2:85814631-85815007	HepG2	liver:	n/a	n/a
17	RCOR1	chr2:85814628-85815121	K562	blood:	n/a	n/a
18	CEBPB	chr2:85814838-85815054	HepG2	liver:	n/a	n/a
19	GATA2	chr2:85814692-85815125	HUVEC	blood vessel:	n/a	n/a
20	GABPA	chr2:85814687-85815041	K562	blood:	n/a	n/a
21	SPI1	chr2:85814722-85815031	K562	blood:	n/a	n/a
22	PML	chr2:85814633-85815145	K562	blood:	n/a	n/a
23	ZNF143	chr2:85814814-85815064	K562	blood:	n/a	n/a
24	MAX	chr2:85814749-85814986	K562	blood:	n/a	n/a
25	ARID3A	chr2:85814653-85815035	K562	blood:	n/a	n/a
26	NFIC	chr2:85814551-85815097	HepG2	liver:	n/a	n/a
27	TRIM28	chr2:85814571-85815120	K562	blood:	n/a	n/a
28	TEAD4	chr2:85814594-85815167	K562	blood:	n/a	n/a
29	GATA1	chr2:85814734-85815114	PBDE	blood:	n/a	n/a
30	TBL1XR1	chr2:85814671-85815127	K562	blood:	n/a	n/a
31	POLR2A	chr2:85814667-85815078	HUVEC	blood vessel:	n/a	n/a
32	EP300	chr2:85814562-85815065	HepG2	liver:	n/a	n/a
33	POLR2A	chr2:85814595-85815219	HL-60	blood:	n/a	n/a
34	REST	chr2:85814716-85815006	K562	blood:	n/a	n/a
35	ATF1	chr2:85814693-85815063	K562	blood:	n/a	n/a
36	MYC	chr2:85814713-85815049	K562	blood:	n/a	n/a
37	NR2F2	chr2:85814635-85815185	HepG2	liver:	n/a	n/a
38	CEBPB	chr2:85814735-85815009	K562	blood:	n/a	n/a
39	POLR2A	chr2:85814761-85815116	K562	blood:	n/a	n/a
40	CUX1	chr2:85814658-85815026	K562	blood:	n/a	n/a
41	HMGN3	chr2:85814761-85814991	K562	blood:	n/a	n/a
42	MYC	chr2:85814679-85815057	K562	blood:	n/a	n/a
43	POLR2A	chr2:85814639-85815146	HUVEC	blood vessel:	n/a	n/a
44	IRF1	chr2:85814692-85815055	K562	blood:	n/a	n/a
45	NR2F2	chr2:85814570-85815144	K562	blood:	n/a	n/a
46	POLR2A	chr2:85814570-85815271	HUVEC	blood vessel:	n/a	n/a
47	MAFF	chr2:85814721-85814999	HepG2	liver:	n/a	n/a
48	NR2F2	chr2:85814607-85815266	HepG2	liver:	n/a	n/a
49	JUND	chr2:85814652-85815096	K562	blood:	n/a	n/a
50	SPI1	chr2:85814653-85815079	GM12891	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:85814940-85814990	HEK293	kidney:	embryo
2	chr2:85814940-85814990	AoSMC	blood vessel:	n/a
3	chr2:85814940-85814990	K562	blood:	n/a
4	chr2:85814940-85814990	LNCaP	prostate:	n/a
5	chr2:85814940-85814990	HUVEC	blood vessel:	n/a
6	chr2:85814940-85814990	PrEC	prostate:	n/a
7	chr2:85814940-85814990	AG09309	skin:	n/a
8	chr2:85814940-85814990	BE2_C	brain:	n/a
9	chr2:85814940-85814990	HRCEpiC	kidney:	n/a
10	chr2:85814940-85814990	ECC-1	luminal epithelium:	n/a
11	chr2:85814940-85814990	Hepatocyte	liver:	n/a
12	chr2:85814940-85814990	HCPEpiC	choroid plexus:	n/a
13	chr2:85814940-85814990	HMEC	breast:	n/a
14	chr2:85814940-85814990	AG10803	skin:	n/a
15	chr2:85814940-85814990	AG09319	gingival:	n/a
16	chr2:85814940-85814990	BJ	skin:	n/a
17	chr2:85814940-85814990	Caco-2	colon:	n/a
18	chr2:85814940-85814990	RPTEC	kidney:	n/a
19	chr2:85814940-85814990	Jurkat	blood:	n/a
20	chr2:85814940-85814990	ovcar-3	ovarian:	n/a
21	chr2:85814940-85814990	HPAEpiC	pulmonary alveolar:	n/a
22	chr2:85814940-85814990	GM12892	blood:	n/a
23	chr2:85814940-85814990	HRPEpiC	eye:	n/a
24	chr2:85814940-85814990	HAEpiC	amniotic membrane:	n/a
25	chr2:85814940-85814990	ProgFib	skin:	n/a
26	chr2:85814940-85814990	AG04449	skin:	fetal
27	chr2:85814940-85814990	MCF10A-Er-Src	breast:	n/a
28	chr2:85814940-85814990	CMK	blood:	n/a
29	chr2:85814940-85814990	H1-hESC	embryonic stem cell:	embryo
30	chr2:85814940-85814990	U87	brain:	n/a
31	chr2:85814940-85814990	NB4	blood:	n/a
32	chr2:85814940-85814990	AG04450	lung:	fetal
33	chr2:85814940-85814990	HCT-116	colon:	n/a
34	chr2:85814940-85814990	PFSK-1	brain:	n/a
35	chr2:85814940-85814990	SK-N-SH	brain:	n/a
36	chr2:85814940-85814990	PANC-1	pancreas:	n/a
37	chr2:85814940-85814990	HRE	kidney:	n/a
38	chr2:85814940-85814990	T-47D	breast:	n/a
39	chr2:85814940-85814990	A549	lung:	n/a
40	chr2:85814940-85814990	GM12878	blood:	n/a
41	chr2:85814940-85814990	HEEpiC	esophagus:	n/a
42	chr2:85814940-85814990	GM19239	blood:	n/a
43	chr2:85814940-85814990	Hela-S3	cervix:	n/a
44	chr2:85814940-85814990	SK-N-MC	brain:	n/a
45	chr2:85814940-85814990	GM12891	blood:	n/a
46	chr2:85814940-85814990	GM06990	blood:	n/a
47	chr2:85814940-85814990	NH-A	brain:	n/a
48	chr2:85814940-85814990	HNPCEpiC	eye:	n/a
49	chr2:85814940-85814990	HCM	heart:	n/a
50	chr2:85814940-85814990	SKMC	muscle:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:85767675..85769335-chr2:85814210..85816393,2	K562	blood:
2	chr2:85764946..85769175-chr2:85814893..85818821,4	K562	blood:

No data

Variant related genes	Relation type
VAMP5	TF binding region
VAMP5	CpG island
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1009	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap]
rs1010	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1011	0.95[ASN][1000 genomes]
rs10172544	0.88[ASN][1000 genomes]
rs10175792	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10176176	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10179195	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10187424	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10198569	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1044158	0.87[GIH][hapmap]
rs1058588	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1078004	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11891260	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12473819	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1254901	0.82[YRI][hapmap]
rs12714145	0.88[ASN][1000 genomes]
rs13394343	0.83[ASN][1000 genomes]
rs1348818	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1446669	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs1561198	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1562323	0.95[ASN][1000 genomes]
rs17026396	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1972297	0.95[ASN][1000 genomes]
rs2028898	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2028900	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2040349	0.82[GIH][hapmap]
rs2043675	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2044474	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2118177	0.82[GIH][hapmap]
rs2166529	0.81[CHB][hapmap];0.81[AMR][1000 genomes]
rs2232748	0.80[JPT][hapmap]
rs2289972	0.86[CHB][hapmap]
rs2366639	0.95[ASN][1000 genomes]
rs2592551	0.86[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap]
rs2886722	0.81[CHB][hapmap]
rs35215812	0.93[ASN][1000 genomes]
rs3731827	0.95[ASN][1000 genomes]
rs3731828	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs3755014	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3755015	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3770098	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs55971080	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59877521	0.83[ASN][1000 genomes]
rs6547620	0.83[ASN][1000 genomes]
rs6547621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6547624	0.93[ASN][1000 genomes]
rs6547629	0.85[GIH][hapmap];0.80[JPT][hapmap];0.85[YRI][hapmap]
rs6705971	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6714157	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6714709	0.83[ASN][1000 genomes]
rs6721924	0.80[ASN][1000 genomes]
rs6731005	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6733550	0.81[GIH][hapmap];0.80[JPT][hapmap]
rs6733913	0.83[ASN][1000 genomes]
rs6735152	0.82[ASN][1000 genomes]
rs6738645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6739015	0.83[ASN][1000 genomes]
rs6743030	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6750847	0.83[ASN][1000 genomes]
rs6757263	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs699664	0.86[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap]
rs7568458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7579147	0.86[CHB][hapmap]
rs7591175	0.81[CHB][hapmap]
rs7593969	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs7605975	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs762684	0.86[CHB][hapmap];0.85[JPT][hapmap]

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10206961	RETSAT	cis	cerebellum	SCAN
rs10206961	MAT2A	cis	cerebellum	SCAN
rs10206961	GGCX	cis	parietal	SCAN
rs10206961	RFK	trans	parietal	SCAN
rs10206961	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs10206961	VAMP5	Cis_1M	lymphoblastoid	RTeQTL
rs10206961	VAMP8	cis	Esophagus Mucosa	GTEx
rs10206961	GGCX	cis	cerebellum	SCAN
rs10206961	VAMP8	cis	uninvolved skin	skin_eQTL
rs10206961	RNF103	cis	parietal	SCAN
rs10206961	VAMP8	cis	lymphoblastoid	seeQTL
rs10206961	GGCX	cis	Whole Blood	GTEx
rs10206961	VAMP8	cis	lesional skin	skin_eQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85812000-85816000	Enhancers	Spleen	Spleen
2	chr2:85812400-85815600	Weak transcription	Aorta	Aorta
3	chr2:85812400-85816000	Enhancers	Primary B cells from cord blood	blood
4	chr2:85812400-85818600	Enhancers	Placenta	Placenta
5	chr2:85812400-85818600	Enhancers	Lung	lung
6	chr2:85812600-85815000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:85812600-85815000	Weak transcription	Fetal Stomach	stomach
8	chr2:85812600-85815200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:85812600-85815400	Enhancers	Primary T cells fromperipheralblood	blood
10	chr2:85812600-85815800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:85812600-85815800	Weak transcription	Ovary	ovary
12	chr2:85812600-85819200	Enhancers	Fetal Muscle Leg	muscle
13	chr2:85812600-85821200	Weak transcription	Fetal Heart	heart
14	chr2:85812800-85815000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr2:85812800-85815200	Weak transcription	Thymus	Thymus
16	chr2:85812800-85815400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr2:85812800-85815600	Weak transcription	Colonic Mucosa	Colon
18	chr2:85812800-85817200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:85812800-85817800	Enhancers	NHLF	lung
20	chr2:85812800-85818800	Enhancers	Psoas Muscle	Psoas
21	chr2:85812800-85819000	Enhancers	Primary hematopoietic stem cells	blood
22	chr2:85813000-85815200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:85813000-85815400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:85813000-85815800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:85813000-85816400	Weak transcription	Gastric	stomach
26	chr2:85813000-85817000	Enhancers	HepG2	liver
27	chr2:85813000-85817200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:85813000-85817200	Weak transcription	Esophagus	oesophagus
29	chr2:85813000-85817200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:85813000-85817400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:85813000-85818200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:85813000-85819600	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr2:85813200-85815000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr2:85813200-85815600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:85813200-85815800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:85813200-85816000	Weak transcription	Brain Substantia Nigra	brain
37	chr2:85813200-85817000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:85813200-85817200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr2:85813200-85817400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:85813200-85817400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:85813200-85817800	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr2:85813200-85817800	Enhancers	Adipose Nuclei	Adipose
43	chr2:85813200-85821400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr2:85813400-85815200	Weak transcription	Brain Angular Gyrus	brain
45	chr2:85813400-85815200	Enhancers	HSMMtube	muscle
46	chr2:85813400-85815400	Weak transcription	Brain Anterior Caudate	brain
47	chr2:85813400-85815600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr2:85813400-85816200	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr2:85813400-85816200	Weak transcription	Osteobl	bone
50	chr2:85813400-85816400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links