Variant report

Variant	rs1673206
Chromosome Location	chr7:138274734-138274735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10155993	0.86[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs10215281	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10227693	0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10232771	0.82[ASN][1000 genomes]
rs10246196	0.85[JPT][hapmap]
rs10247380	0.87[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10248731	0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10249171	0.85[YRI][hapmap]
rs10256619	0.87[YRI][hapmap]
rs10261236	0.87[YRI][hapmap]
rs10281429	0.82[YRI][hapmap]
rs1030961	0.86[ASN][1000 genomes]
rs1077772	0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs1116324	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11976614	0.80[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap]
rs12112459	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12666310	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1371463	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1421604	0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1544733	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1614641	0.95[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1616318	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1659830	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1659831	0.82[EUR][1000 genomes]
rs1659832	0.89[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes]
rs1673203	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1673204	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1673205	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs1673207	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1673211	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17364560	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17461551	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1813003	0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs1874326	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs2029814	0.84[JPT][hapmap]
rs2029815	0.85[JPT][hapmap]
rs2353351	0.84[JPT][hapmap]
rs2353354	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2353355	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3757381	0.84[ASN][1000 genomes]
rs3778705	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3807155	0.80[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.90[ASN][1000 genomes]
rs3807156	0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs3807157	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55723768	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56092804	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57407834	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58562866	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62485261	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62485263	0.87[ASN][1000 genomes]
rs62485264	0.89[ASN][1000 genomes]
rs62487615	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62487616	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62487619	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6467776	0.81[ASN][1000 genomes]
rs6467778	0.87[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6467780	0.86[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs6467782	0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6467783	0.87[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6948094	0.83[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs6954285	0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6959574	0.87[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6963539	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6970175	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6974877	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6978524	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs728092	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs749546	0.95[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7795981	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs888609	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9791462	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9791634	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs985299	0.87[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030956	chr7:138163169-138579519	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1673206	SSBP1	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:138256400-138276600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr7:138265400-138276800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:138266200-138275600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:138270800-138274800	Weak transcription	GM12878-XiMat	blood
5	chr7:138270800-138276600	Weak transcription	K562	blood
6	chr7:138272400-138276400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:138272400-138278200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:138272600-138274800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr7:138272600-138275000	Weak transcription	Fetal Stomach	stomach
10	chr7:138272600-138276200	Weak transcription	Fetal Intestine Small	intestine
11	chr7:138272600-138276600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr7:138272600-138280400	Weak transcription	Thymus	Thymus
13	chr7:138272600-138286200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:138272800-138275200	Weak transcription	Liver	Liver
15	chr7:138272800-138276400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr7:138272800-138278400	Weak transcription	Fetal Intestine Large	intestine
17	chr7:138273000-138274800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr7:138273000-138274800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:138273000-138274800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr7:138273000-138275600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:138273000-138276400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr7:138273000-138278600	Weak transcription	Fetal Brain Female	brain
23	chr7:138273000-138284000	Weak transcription	Fetal Kidney	kidney
24	chr7:138273000-138285000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:138273000-138286200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:138273000-138286200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:138273200-138274800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:138273200-138276400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:138273400-138275400	Weak transcription	Primary T cells from cord blood	blood
30	chr7:138273400-138277000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:138273600-138286800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:138274200-138274800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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