Variant report

Variant	rs1380380
Chromosome Location	chr7:16813427-16813428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:16812942-16814461	PBDE	blood:	n/a	n/a
2	GATA1	chr7:16812697-16814689	PBDE	blood:	n/a	chr7:16814259-16814268 chr7:16813440-16813447 chr7:16813440-16813449 chr7:16814258-16814270 chr7:16814259-16814269 chr7:16813439-16813449 chr7:16814256-16814272 chr7:16813436-16813452 chr7:16813440-16813447 chr7:16813433-16813454 chr7:16813440-16813447

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:16793468..16795066-chr7:16813077..16814664,2	MCF-7	breast:
2	chr7:16808766..16811387-chr7:16812487..16815098,2	K562	blood:

Variant related genes	Relation type
TSPAN13	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs706057	0.84[CHD][hapmap]
rs706059	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs706063	0.81[EUR][1000 genomes]
rs706065	0.81[CEU][hapmap];0.80[MEX][hapmap];0.82[EUR][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	nsv1028125	chr7:16529160-16847225	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1024059	chr7:16639432-16836425	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1380380	AGR2	cis	cerebellum	SCAN
rs1380380	TWIST1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16795000-16828400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:16796600-16816200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:16800600-16825600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:16802800-16817800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr7:16803600-16818000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:16803800-16825600	Weak transcription	Fetal Intestine Small	intestine
7	chr7:16805000-16832400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:16805200-16813600	Weak transcription	Left Ventricle	heart
9	chr7:16805200-16815600	Weak transcription	Fetal Brain Female	brain
10	chr7:16805200-16815800	Weak transcription	Fetal Intestine Large	intestine
11	chr7:16806400-16821400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr7:16806800-16815200	Weak transcription	Pancreas	Pancrea
13	chr7:16810800-16815400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr7:16810800-16823200	Weak transcription	Psoas Muscle	Psoas
15	chr7:16810800-16825000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr7:16811000-16814800	Strong transcription	Primary B cells from cord blood	blood
17	chr7:16811000-16815400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr7:16811000-16817800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr7:16811200-16814000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:16811200-16816000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr7:16811400-16815400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr7:16811400-16815400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr7:16811400-16815400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr7:16811400-16821800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr7:16811400-16833600	Weak transcription	Fetal Muscle Leg	muscle
26	chr7:16811600-16814000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:16811600-16814400	Weak transcription	NHEK	skin
28	chr7:16811600-16817800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:16811600-16820800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr7:16811600-16825000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:16811800-16824800	Weak transcription	Adipose Nuclei	Adipose
32	chr7:16812000-16817800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:16812200-16813600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr7:16812400-16821600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr7:16812800-16821000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:16813000-16813800	Enhancers	Fetal Heart	heart
37	chr7:16813000-16813800	Enhancers	Stomach Mucosa	stomach
38	chr7:16813000-16814000	Enhancers	Fetal Brain Male	brain
39	chr7:16813000-16814000	Enhancers	Fetal Lung	lung
40	chr7:16813000-16814000	Enhancers	K562	blood
41	chr7:16813000-16814200	Enhancers	Gastric	stomach
42	chr7:16813000-16814200	Enhancers	Right Ventricle	heart
43	chr7:16813000-16814200	Enhancers	Osteobl	bone

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