Variant report

Variant	rs1374370
Chromosome Location	chr2:85818273-85818274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:85818160-85818310	MCF-7	breast:	n/a	n/a
2	RCOR1	chr2:85817003-85818311	IMR90	lung:	n/a	n/a
3	NR2F2	chr2:85816992-85818568	MCF-7	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85767293..85770194-chr2:85815993..85818775,2	MCF-7	breast:
2	chr2:85765298..85767706-chr2:85816811..85818953,3	MCF-7	breast:
3	chr2:85773637..85776007-chr2:85816213..85818634,2	K562	blood:
4	chr2:85786918..85789789-chr2:85816753..85818316,2	K562	blood:
5	chr2:85786482..85790460-chr2:85816178..85820132,9	MCF-7	breast:
6	chr2:85764946..85769175-chr2:85814893..85818821,4	K562	blood:
7	chr2:85787036..85790013-chr2:85817133..85820348,4	MCF-7	breast:

No data

Variant related genes	Relation type
RNF181	TF binding region
VAMP5	TF binding region
ENSG00000168906	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000115486	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11891495	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12463933	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs14976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17508809	1.00[JPT][hapmap]
rs17508843	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2289976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34623563	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56192500	0.80[ASN][1000 genomes]
rs62166769	0.81[ASN][1000 genomes]
rs62166770	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62166779	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72843872	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7569073	1.00[JPT][hapmap]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1374370	RNF103	cis	parietal	SCAN
rs1374370	VAMP8	cis	parietal	SCAN
rs1374370	GGCX	cis	cerebellum	SCAN
rs1374370	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs1374370	VAMP5	cis	lymphoblastoid	seeQTL
rs1374370	VAMP5	Cis_1M	lymphoblastoid	RTeQTL
rs1374370	GGCX	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85812400-85818600	Enhancers	Placenta	Placenta
2	chr2:85812400-85818600	Enhancers	Lung	lung
3	chr2:85812600-85819200	Enhancers	Fetal Muscle Leg	muscle
4	chr2:85812600-85821200	Weak transcription	Fetal Heart	heart
5	chr2:85812800-85818800	Enhancers	Psoas Muscle	Psoas
6	chr2:85812800-85819000	Enhancers	Primary hematopoietic stem cells	blood
7	chr2:85813000-85819600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr2:85813200-85821400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:85813400-85818400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr2:85813400-85819000	Enhancers	Right Atrium	heart
11	chr2:85813600-85821400	Weak transcription	Fetal Intestine Large	intestine
12	chr2:85813800-85820000	Weak transcription	Fetal Intestine Small	intestine
13	chr2:85814000-85821600	Weak transcription	Small Intestine	intestine
14	chr2:85814200-85818800	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr2:85814600-85819400	Enhancers	Fetal Lung	lung
16	chr2:85814600-85819600	Enhancers	Left Ventricle	heart
17	chr2:85814600-85819600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr2:85814800-85819400	Enhancers	Brain Hippocampus Middle	brain
19	chr2:85815000-85821400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr2:85815000-85821600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr2:85815200-85818800	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr2:85815200-85819000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:85815200-85819000	Weak transcription	Fetal Stomach	stomach
24	chr2:85815200-85819200	Enhancers	Fetal Muscle Trunk	muscle
25	chr2:85815200-85821600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:85815400-85821200	Weak transcription	Dnd41	blood
27	chr2:85815400-85821400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr2:85815400-85821400	Weak transcription	GM12878-XiMat	blood
29	chr2:85815600-85818400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:85815600-85818400	Enhancers	Liver	Liver
31	chr2:85815600-85819200	Enhancers	Brain Cingulate Gyrus	brain
32	chr2:85815600-85821400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:85815600-85821400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:85815600-85821400	Weak transcription	Hela-S3	cervix
35	chr2:85815800-85819000	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr2:85815800-85819000	Enhancers	Ovary	ovary
37	chr2:85815800-85819200	Enhancers	Brain Angular Gyrus	brain
38	chr2:85815800-85821400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:85815800-85821600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr2:85816000-85819200	Enhancers	Brain Substantia Nigra	brain
41	chr2:85816000-85820200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:85816000-85821400	Weak transcription	Fetal Kidney	kidney
43	chr2:85816000-85821400	Weak transcription	Thymus	Thymus
44	chr2:85816200-85819600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:85816200-85821400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:85816400-85819000	Enhancers	Gastric	stomach
47	chr2:85816600-85819600	Enhancers	Colon Smooth Muscle	Colon
48	chr2:85816800-85819000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr2:85817000-85818400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:85817000-85819000	Enhancers	Fetal Thymus	thymus

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