Variant report

Variant	rs550164
Chromosome Location	chr11:120002727-120002728
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:119993537..119997499-chr11:119998076..120003019,6	K562	blood:

Variant related genes	Relation type
ENSG00000137699	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1790476	0.89[EUR][1000 genomes]
rs2444240	0.87[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs470370	0.81[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs470373	0.85[ASN][1000 genomes]
rs470392	0.86[CHB][hapmap]
rs470411	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs470645	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs470725	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs470876	0.81[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap]
rs470941	0.94[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs471001	0.82[ASN][1000 genomes]
rs488672	0.86[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs531260	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs533636	0.87[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap]
rs561498	1.00[CEU][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs566935	0.82[JPT][hapmap]
rs573211	0.80[ASN][1000 genomes]
rs590843	0.86[CHB][hapmap]
rs605374	0.86[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs670855	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][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	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1050132	chr11:119976310-120010437	Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs550164	TRIM29	cis	Artery Tibial	GTEx
rs550164	THY1	cis	cerebellum	SCAN
rs550164	SORL1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119997600-120003200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
2	chr11:119999000-120006400	Enhancers	Placenta	Placenta
3	chr11:120000200-120003400	Transcr. at gene 5' and 3'	Esophagus	oesophagus
4	chr11:120000400-120008400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr11:120000600-120002800	Weak transcription	Colonic Mucosa	Colon
6	chr11:120000600-120002800	Genic enhancers	NHEK	skin
7	chr11:120000600-120006400	Weak transcription	Fetal Thymus	thymus
8	chr11:120000800-120003200	Genic enhancers	HMEC	breast
9	chr11:120001400-120005200	Weak transcription	Hela-S3	cervix
10	chr11:120001400-120007800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:120002000-120006000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:120002200-120003400	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr11:120002400-120003800	Enhancers	Pancreas	Pancrea
14	chr11:120002600-120002800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:120002600-120003000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:120002600-120003200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:120002600-120003400	Enhancers	Fetal Intestine Large	intestine
18	chr11:120002600-120003400	Enhancers	Fetal Intestine Small	intestine

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