Variant report

Variant	rs628885
Chromosome Location	chr7:69163557-69163558
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1003404	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10260553	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[ASN][1000 genomes]
rs12670658	0.92[ASN][1000 genomes]
rs1548748	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17140890	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1990444	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210602	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210605	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215354	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2533436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2533437	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851486	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851493	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2851519	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2851520	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34701787	0.87[ASN][1000 genomes]
rs41848	0.92[ASN][1000 genomes]
rs41854	0.92[ASN][1000 genomes]
rs41857	0.92[ASN][1000 genomes]
rs4717522	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548556	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569334	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633927	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953849	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs917617	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916011	chr7:68942155-69330800	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv428169	chr7:69021482-69196743	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv831021	chr7:69122169-69364491	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1021538	chr7:69130236-69575753	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv538917	chr7:69130236-69575753	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv817276	chr7:69130237-69736834	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1034380	chr7:69137914-69171449	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
8	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs628885	STAG3L4	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69148400-69166200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:69153600-69167400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:69156600-69166600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr7:69156800-69166400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:69157200-69167800	Weak transcription	Fetal Stomach	stomach
6	chr7:69159200-69167800	Weak transcription	Fetal Lung	lung
7	chr7:69159400-69163600	Enhancers	Fetal Thymus	thymus
8	chr7:69161000-69164200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:69161400-69171000	Weak transcription	Left Ventricle	heart
10	chr7:69161400-69171200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:69161600-69166800	Weak transcription	Brain Anterior Caudate	brain
12	chr7:69161600-69173400	Weak transcription	Right Atrium	heart
13	chr7:69161800-69163600	Enhancers	Dnd41	blood
14	chr7:69161800-69167600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr7:69161800-69170400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr7:69162000-69186200	Weak transcription	Primary B cells from cord blood	blood
17	chr7:69162200-69170800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr7:69162400-69163800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr7:69162400-69165000	Weak transcription	Brain Germinal Matrix	brain
20	chr7:69162400-69165000	Weak transcription	Fetal Brain Female	brain
21	chr7:69162400-69168000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:69162600-69163800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:69162600-69165400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:69162600-69168800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:69162800-69166000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:69162800-69168000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr7:69163000-69166200	Enhancers	GM12878-XiMat	blood
28	chr7:69163000-69167400	Weak transcription	Colon Smooth Muscle	Colon
29	chr7:69163200-69164000	Enhancers	Liver	Liver
30	chr7:69163400-69164600	Enhancers	Fetal Brain Male	brain

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