Variant report

Variant	rs12700324
Chromosome Location	chr7:21937156-21937157
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12154628	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12700323	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12700325	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17361723	0.83[AMR][1000 genomes]
rs34245961	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34894075	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35469450	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35907340	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4534048	0.88[EUR][1000 genomes]
rs62445884	0.85[AMR][1000 genomes]
rs6949101	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6953368	0.84[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs6963989	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6979604	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018133	chr7:21740118-22055283	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv830922	chr7:21793386-21964675	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1027453	chr7:21918474-21982448	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12700324	SP8	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21907400-21937200	Weak transcription	Fetal Thymus	thymus
2	chr7:21910000-21939400	Weak transcription	Left Ventricle	heart
3	chr7:21911200-21938400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr7:21917000-21938400	Weak transcription	Fetal Intestine Small	intestine
5	chr7:21923000-21937800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:21923200-21938600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:21924000-21937600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:21924400-21937800	Weak transcription	NHEK	skin
9	chr7:21924400-21945400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:21926400-21937800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr7:21926600-21942600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr7:21926800-21938000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr7:21926800-21939200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr7:21927800-21937600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:21927800-21937800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:21927800-21938400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr7:21927800-21940200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:21928000-21937200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr7:21928000-21942600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr7:21928200-21937600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr7:21928200-21938600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:21928200-21939600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:21928800-21938400	Weak transcription	NHDF-Ad	bronchial
24	chr7:21929200-21938000	Weak transcription	Fetal Lung	lung
25	chr7:21929800-21938000	Weak transcription	Right Ventricle	heart
26	chr7:21930000-21937800	Weak transcription	Gastric	stomach
27	chr7:21930400-21937600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:21930800-21938400	Weak transcription	Esophagus	oesophagus
29	chr7:21931000-21942400	Weak transcription	Fetal Kidney	kidney
30	chr7:21931400-21937800	Weak transcription	Fetal Stomach	stomach
31	chr7:21932600-21937800	Weak transcription	Fetal Heart	heart
32	chr7:21932600-21938000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr7:21932600-21938200	Weak transcription	Hela-S3	cervix
34	chr7:21932600-21938400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:21932600-21938400	Weak transcription	Brain Anterior Caudate	brain
36	chr7:21932600-21942000	Weak transcription	Brain Germinal Matrix	brain
37	chr7:21932600-21951000	Weak transcription	HSMM	muscle
38	chr7:21932800-21938800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr7:21933000-21963200	Weak transcription	A549	lung
40	chr7:21933600-21939000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr7:21934000-21950400	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr7:21934200-21951600	Weak transcription	Fetal Brain Male	brain
43	chr7:21934600-21937400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:21935200-21937600	Weak transcription	Thymus	Thymus
45	chr7:21935200-21942200	Weak transcription	HMEC	breast
46	chr7:21936000-21937200	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr7:21936200-21937800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr7:21936400-21937600	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr7:21936400-21937800	Enhancers	Primary B cells from peripheral blood	blood
50	chr7:21936400-21938000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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