Variant report

Variant	rs488672
Chromosome Location	chr11:120047745-120047746
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:120047526..120050169-chr11:120053721..120056397,2	K562	blood:
2	chr11:120045083..120049940-chr11:120105955..120109053,5	K562	blood:
3	chr11:120045369..120049048-chr11:120049155..120051073,3	K562	blood:

Variant related genes	Relation type
ENSG00000137699	Chromatin interaction
ENSG00000137709	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1790476	0.90[EUR][1000 genomes]
rs2444240	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs470370	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs470373	0.95[ASN][1000 genomes]
rs470411	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs470645	1.00[JPT][hapmap]
rs470725	0.80[EUR][1000 genomes]
rs470876	0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs470941	0.87[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs471001	0.85[ASN][1000 genomes]
rs4938790	0.92[ASN][1000 genomes]
rs521556	0.97[ASN][1000 genomes]
rs528147	0.94[ASN][1000 genomes]
rs529657	0.97[ASN][1000 genomes]
rs529681	0.94[ASN][1000 genomes]
rs531260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533636	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs550164	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]
rs561498	0.86[CEU][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs566935	0.81[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs573211	1.00[ASN][1000 genomes]
rs605374	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs670855	0.86[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs896691	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv428581	chr11:120006048-120167603	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv518464	chr11:120040442-120109967	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs488672	THY1	cis	cerebellum	SCAN
rs488672	TRIM29	cis	Artery Tibial	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120040600-120049000	Weak transcription	Colon Smooth Muscle	Colon
2	chr11:120040600-120049600	Weak transcription	Right Atrium	heart
3	chr11:120043600-120048200	Weak transcription	Brain Hippocampus Middle	brain
4	chr11:120043600-120051000	Weak transcription	HepG2	liver
5	chr11:120043600-120057000	Weak transcription	Esophagus	oesophagus
6	chr11:120043800-120050400	Weak transcription	Liver	Liver
7	chr11:120044400-120048200	Weak transcription	Brain Substantia Nigra	brain
8	chr11:120044400-120049600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:120044400-120055200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:120044600-120048200	Weak transcription	Brain Anterior Caudate	brain
11	chr11:120044600-120048200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:120044600-120051400	Weak transcription	Fetal Kidney	kidney
13	chr11:120044600-120051800	Weak transcription	Pancreas	Pancrea
14	chr11:120044800-120047800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr11:120045000-120048000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:120045000-120048200	Weak transcription	Fetal Stomach	stomach
17	chr11:120045000-120048400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:120045000-120049000	Weak transcription	Fetal Lung	lung
19	chr11:120045000-120051200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr11:120046200-120049200	Weak transcription	Fetal Intestine Small	intestine
21	chr11:120046200-120053000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr11:120046400-120049600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr11:120046400-120051000	Weak transcription	Fetal Intestine Large	intestine
24	chr11:120046400-120051600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr11:120046800-120055800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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