Variant report

Variant	rs7304944
Chromosome Location	chr12:56958447-56958448
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10783792	1.00[ASN][1000 genomes]
rs10876910	1.00[ASN][1000 genomes]
rs11171817	0.96[MKK][hapmap]
rs11171935	1.00[MKK][hapmap]
rs12232026	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs12302233	0.89[ASN][1000 genomes]
rs2638287	0.82[JPT][hapmap]
rs2657896	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs2694917	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2888045	0.99[ASN][1000 genomes]
rs3759091	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4759251	0.95[ASN][1000 genomes]
rs7133264	0.97[ASN][1000 genomes]
rs774211	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs813497	0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv899106	chr12:56905558-57004668	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv3375110	chr12:56956280-56965593	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7304944	SPRYD4	cis	multi-tissue	Pritchard
rs7304944	SPRYD4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56917200-56959200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr12:56922400-56959200	Weak transcription	Fetal Kidney	kidney
3	chr12:56923800-56959400	Weak transcription	Aorta	Aorta
4	chr12:56924800-56959200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:56925000-56959200	Weak transcription	HSMMtube	muscle
6	chr12:56931400-56959400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:56931600-56965000	Weak transcription	Hela-S3	cervix
8	chr12:56932200-56959200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:56933200-56959000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr12:56933200-56959200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:56933400-56959200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr12:56935600-56959200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:56937200-56959200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:56946600-56959200	Weak transcription	Spleen	Spleen
15	chr12:56947200-56959200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:56948200-56959200	Weak transcription	Colonic Mucosa	Colon
17	chr12:56948600-56981200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:56950000-56959600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:56950800-56975000	Weak transcription	Esophagus	oesophagus
20	chr12:56951000-56959600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:56951200-56959200	Weak transcription	Fetal Thymus	thymus
22	chr12:56951400-56959200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:56951400-56963600	Weak transcription	Brain Anterior Caudate	brain
24	chr12:56952600-56966200	Weak transcription	Fetal Brain Female	brain
25	chr12:56952600-56974800	Weak transcription	Pancreas	Pancrea
26	chr12:56953200-56959200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:56953200-56981200	Weak transcription	Brain Substantia Nigra	brain
28	chr12:56954400-56974800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr12:56954600-56958800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:56954600-56959000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:56954600-56959200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:56954600-56993400	Weak transcription	Fetal Brain Male	brain
33	chr12:56955000-56958600	Strong transcription	Fetal Intestine Small	intestine
34	chr12:56955000-56959000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr12:56955000-56959200	Weak transcription	Fetal Heart	heart
36	chr12:56955000-56959400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr12:56955000-56959400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:56955600-56958800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:56955600-56958800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:56955800-56958600	Strong transcription	Fetal Muscle Leg	muscle
41	chr12:56955800-56959000	Strong transcription	A549	lung
42	chr12:56955800-56959000	Strong transcription	Osteobl	bone
43	chr12:56955800-56959200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr12:56955800-56959200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:56955800-56959200	Weak transcription	Thymus	Thymus
46	chr12:56955800-56959400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr12:56955800-56959600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr12:56956000-56958600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:56956000-56958800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:56956000-56959200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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