Variant report

Variant	rs1005510
Chromosome Location	chr11:57367222-57367223
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	chr11:57363269..57366608-chr11:57366625..57370345,5	K562	blood:

Variant related genes	Relation type
ENSG00000149131	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1005511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12793139	0.81[CHB][hapmap]
rs1812005	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244169	0.86[JPT][hapmap]
rs2432810	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508439	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2508442	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2509897	0.82[JPT][hapmap]
rs2511985	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2511988	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2511990	0.86[JPT][hapmap]
rs2511997	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2729376	0.86[JPT][hapmap]
rs517638	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv897588	chr11:57364381-57373478	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1005510	YPEL4	cis	lymphoblastoid	seeQTL
rs1005510	MED19	cis	cerebellum	SCAN
rs1005510	GATA6	trans	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57365200-57369000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:57366200-57379000	Weak transcription	Gastric	stomach
3	chr11:57366400-57367400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:57366400-57367400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:57366400-57367600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:57366400-57373200	Weak transcription	Spleen	Spleen
7	chr11:57366400-57381800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:57366400-57385800	Weak transcription	Esophagus	oesophagus
9	chr11:57366600-57367400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:57366600-57367400	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr11:57366600-57367400	Active TSS	Stomach Smooth Muscle	stomach
12	chr11:57366600-57367600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr11:57366600-57369400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:57366600-57373200	Weak transcription	Brain Angular Gyrus	brain
15	chr11:57366600-57378800	Weak transcription	Colonic Mucosa	Colon
16	chr11:57366600-57382600	Weak transcription	Brain Substantia Nigra	brain
17	chr11:57366600-57384400	Weak transcription	Pancreas	Pancrea
18	chr11:57366800-57367400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:57366800-57367400	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr11:57366800-57367400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr11:57366800-57367400	Weak transcription	Aorta	Aorta
22	chr11:57366800-57367400	Weak transcription	Lung	lung
23	chr11:57366800-57367400	Weak transcription	Ovary	ovary
24	chr11:57366800-57367600	Genic enhancers	Adipose Nuclei	Adipose
25	chr11:57366800-57367600	Weak transcription	Right Atrium	heart
26	chr11:57366800-57367800	Weak transcription	Left Ventricle	heart
27	chr11:57366800-57368000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:57366800-57369400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr11:57366800-57369400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr11:57366800-57369400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr11:57366800-57369400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr11:57366800-57369400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr11:57366800-57371400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr11:57366800-57371400	Weak transcription	Placenta	Placenta
35	chr11:57366800-57371400	Weak transcription	Fetal Thymus	thymus
36	chr11:57366800-57373200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr11:57366800-57373800	Weak transcription	Brain Hippocampus Middle	brain
38	chr11:57366800-57380800	Weak transcription	Brain Anterior Caudate	brain
39	chr11:57366800-57381600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr11:57366800-57381600	Weak transcription	Osteobl	bone
41	chr11:57366800-57386600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr11:57366800-57388800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr11:57367000-57367400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:57367000-57367400	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr11:57367000-57367400	Enhancers	Brain Germinal Matrix	brain
46	chr11:57367000-57367400	Enhancers	Fetal Lung	lung
47	chr11:57367000-57367800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr11:57367000-57368000	Transcr. at gene 5' and 3'	Liver	Liver
49	chr11:57367000-57373200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr11:57367000-57373400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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