Variant report

Variant	rs895729
Chromosome Location	chr11:45679197-45679198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45677224..45679884-chr11:45774991..45777658,2	MCF-7	breast:
2	chr11:45678783..45681662-chr11:45685006..45688205,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175264	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10769160	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1078720	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11038608	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs12804655	0.96[ASN][1000 genomes]
rs1348963	0.91[EUR][1000 genomes]
rs1447569	0.92[JPT][hapmap]
rs34264431	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs36106594	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4148893	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4148894	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4148897	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4148904	1.00[JPT][hapmap]
rs45486999	0.99[ASN][1000 genomes]
rs45604433	0.98[ASN][1000 genomes]
rs4756016	0.81[EUR][1000 genomes]
rs55681357	0.99[ASN][1000 genomes]
rs7121696	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs750398	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs895734	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897311	chr11:45663568-45691118	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv897312	chr11:45663568-45699134	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv897313	chr11:45670395-45699134	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv554197	chr11:45673014-45679212	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv554198	chr11:45674266-45684117	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs895729	CHST1	cis	parietal	SCAN
rs895729	ACP2	cis	parietal	SCAN
rs895729	OR4C45	cis	cerebellum	SCAN
rs895729	F2	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45665600-45680000	Weak transcription	Gastric	stomach
2	chr11:45670000-45680200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:45674200-45679800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:45674600-45679800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:45675600-45679800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:45676800-45680000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:45677000-45679800	Weak transcription	Osteobl	bone
8	chr11:45677000-45680000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:45677200-45679800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr11:45677200-45679800	Weak transcription	NH-A	brain
11	chr11:45677200-45680000	Weak transcription	Brain Anterior Caudate	brain
12	chr11:45677400-45679200	Weak transcription	Right Ventricle	heart
13	chr11:45677400-45679200	Weak transcription	Spleen	Spleen
14	chr11:45677400-45679400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:45677400-45679400	Weak transcription	Brain Substantia Nigra	brain
16	chr11:45677400-45679400	Weak transcription	Left Ventricle	heart
17	chr11:45677400-45679600	Weak transcription	Ovary	ovary
18	chr11:45677400-45679800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:45677400-45679800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr11:45677400-45679800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr11:45677400-45680000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:45677400-45680000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr11:45677400-45680000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr11:45677400-45680000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr11:45677600-45680200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:45677600-45680400	Weak transcription	Fetal Brain Female	brain
27	chr11:45677800-45679200	Weak transcription	Fetal Brain Male	brain
28	chr11:45677800-45679600	Weak transcription	Brain Angular Gyrus	brain
29	chr11:45677800-45679600	Weak transcription	Brain Hippocampus Middle	brain
30	chr11:45677800-45680600	Weak transcription	Brain Germinal Matrix	brain
31	chr11:45678200-45680000	Weak transcription	Lung	lung
32	chr11:45678200-45684200	Enhancers	HUVEC	blood vessel
33	chr11:45678400-45685200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:45678600-45679600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:45678600-45680000	Enhancers	Brain Cingulate Gyrus	brain
36	chr11:45678600-45680400	Enhancers	Fetal Muscle Trunk	muscle
37	chr11:45678600-45683600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr11:45679000-45680800	Enhancers	Fetal Muscle Leg	muscle
39	chr11:45679000-45684200	Enhancers	Dnd41	blood

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