Variant report

Variant	rs1000665
Chromosome Location	chr11:45286085-45286086
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:45200307..45202663-chr11:45284381..45286142,2	MCF-7	breast:
2	chr11:45167741..45169495-chr11:45284745..45287574,2	MCF-7	breast:
3	chr11:45284512..45286727-chr11:45305092..45307914,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000019485	Chromatin interaction
ENSG00000019505	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10769137	0.87[EUR][1000 genomes]
rs10838436	1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.91[MKK][hapmap];0.96[ASN][1000 genomes]
rs10838439	0.82[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11038366	0.90[CHB][hapmap]
rs11038371	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11601021	0.90[CHB][hapmap]
rs12278234	0.90[CHB][hapmap]
rs12362429	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12362444	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12362448	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2863179	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2863183	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3180446	0.90[CHB][hapmap]
rs4755308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4755940	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7124508	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs751197	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs751198	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs751995	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs7935226	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7942231	0.85[AMR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1000665	SYT13	cis	normal skin	skin_eQTL
rs1000665	SYT13	cis	cerebellum	SCAN
rs1000665	SYT13	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45281600-45286200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr11:45282200-45286800	Weak transcription	Pancreas	Pancrea
3	chr11:45282600-45286800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:45282600-45286800	Weak transcription	Fetal Brain Female	brain
5	chr11:45282600-45288800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:45283400-45288800	Enhancers	Fetal Intestine Small	intestine
7	chr11:45284200-45287600	Enhancers	Duodenum Mucosa	Duodenum
8	chr11:45284400-45290200	Enhancers	Fetal Intestine Large	intestine
9	chr11:45284800-45286600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr11:45285000-45286200	Enhancers	A549	lung
11	chr11:45285400-45288600	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr11:45285400-45289000	Enhancers	Stomach Mucosa	stomach
13	chr11:45285600-45287800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:45285800-45287400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr11:45285800-45287400	Enhancers	Small Intestine	intestine
16	chr11:45285800-45287800	Enhancers	HMEC	breast
17	chr11:45285800-45288200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:45286000-45286200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:45286000-45286200	Flanking Active TSS	HSMM	muscle
20	chr11:45286000-45286200	Enhancers	NH-A	brain
21	chr11:45286000-45286400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:45286000-45286400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:45286000-45286400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:45286000-45286400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr11:45286000-45286800	Enhancers	HSMMtube	muscle
26	chr11:45286000-45287000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr11:45286000-45287200	Enhancers	Colonic Mucosa	Colon
28	chr11:45286000-45287200	Enhancers	Hela-S3	cervix
29	chr11:45286000-45287200	Enhancers	NHDF-Ad	bronchial
30	chr11:45286000-45287600	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr11:45286000-45288200	Enhancers	Osteobl	bone

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