Variant report

Variant	rs2290837
Chromosome Location	chr7:16816000-16816001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10233465	0.83[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs10238328	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1149519	0.86[ASN][1000 genomes]
rs1149522	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1149524	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1149526	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12530923	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12535558	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12540544	0.96[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13232235	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13244013	0.89[ASN][1000 genomes]
rs2085706	0.81[ASN][1000 genomes]
rs2290836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34614062	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3779051	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs3807490	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs3807492	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3807493	0.84[CEU][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3807509	0.84[CHB][hapmap]
rs3823652	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4400279	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4721538	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4721539	0.95[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62441050	0.93[ASN][1000 genomes]
rs6461276	0.88[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6951449	0.83[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6962578	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs6975847	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs747347	0.96[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7781646	0.85[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7808455	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7809197	0.81[ASN][1000 genomes]
rs818803	0.85[CHB][hapmap];0.91[JPT][hapmap]

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
rs2290837	TWIST1	cis	cerebellum	SCAN
rs2290837	TSPAN13	cis	parietal	SCAN

Chromatin state (count:48 , 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	chr7:16806400-16821400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr7:16810800-16823200	Weak transcription	Psoas Muscle	Psoas
10	chr7:16810800-16825000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:16811000-16817800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr7:16811200-16816000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr7:16811400-16821800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:16811400-16833600	Weak transcription	Fetal Muscle Leg	muscle
15	chr7:16811600-16817800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr7:16811600-16820800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:16811600-16825000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:16811800-16824800	Weak transcription	Adipose Nuclei	Adipose
19	chr7:16812000-16817800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:16812400-16821600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr7:16812800-16821000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:16813800-16816600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr7:16813800-16825000	Weak transcription	Stomach Mucosa	stomach
24	chr7:16814000-16834600	Weak transcription	Fetal Brain Male	brain
25	chr7:16814200-16818000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:16814200-16821200	Weak transcription	Left Ventricle	heart
27	chr7:16814200-16824800	Weak transcription	Osteobl	bone
28	chr7:16814200-16825400	Weak transcription	Gastric	stomach
29	chr7:16814200-16826400	Weak transcription	Right Ventricle	heart
30	chr7:16814400-16843800	Weak transcription	Small Intestine	intestine
31	chr7:16815000-16817600	Strong transcription	Primary B cells from cord blood	blood
32	chr7:16815000-16838000	Weak transcription	K562	blood
33	chr7:16815200-16816000	Enhancers	Pancreas	Pancrea
34	chr7:16815400-16816200	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr7:16815400-16816200	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr7:16815400-16816200	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr7:16815400-16823000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr7:16815600-16816000	Enhancers	H1 Cell Line	embryonic stem cell
39	chr7:16815600-16816000	Enhancers	Fetal Brain Female	brain
40	chr7:16815600-16816200	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr7:16815800-16816000	Enhancers	Lung	lung
42	chr7:16815800-16816200	Strong transcription	Fetal Intestine Large	intestine
43	chr7:16815800-16817000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr7:16815800-16817800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr7:16816000-16817800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr7:16816000-16819000	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr7:16816000-16819800	Weak transcription	Lung	lung
48	chr7:16816000-16825000	Weak transcription	Fetal Brain Female	brain

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