Variant report

Variant	rs11120070
Chromosome Location	chr1:213155566-213155567
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:213153525..213156288-chr1:213157594..213160257,3	K562	blood:
2	chr1:213145484..213147806-chr1:213154081..213156986,2	K562	blood:
3	chr1:213143678..213151221-chr1:213151923..213156487,9	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1045868	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10735511	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10746440	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10779597	0.81[ASN][1000 genomes]
rs10779598	1.00[JPT][hapmap]
rs10864031	0.83[ASN][1000 genomes]
rs10864032	0.89[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10864033	0.89[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11120076	0.89[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11120080	0.84[ASN][1000 genomes]
rs11120082	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs11120084	0.81[AFR][1000 genomes]
rs11586518	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12026770	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12122955	0.87[ASN][1000 genomes]
rs12563167	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3002284	0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs3104207	0.87[ASN][1000 genomes]
rs3123307	0.84[ASN][1000 genomes]
rs3738806	0.89[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4951660	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6540777	0.86[AFR][1000 genomes]
rs6697921	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs7537285	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7540350	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008594	chr1:213110654-213236750	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv11434	chr1:213131581-213156027	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11120070	ANGEL2	cis	cerebellum	SCAN
rs11120070	BATF3	cis	parietal	SCAN
rs11120070	ANGEL2	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213133600-213161600	Weak transcription	Fetal Intestine Large	intestine
2	chr1:213146600-213157200	Genic enhancers	Fetal Muscle Leg	muscle
3	chr1:213148400-213165400	Weak transcription	Fetal Kidney	kidney
4	chr1:213149800-213156000	Genic enhancers	Fetal Muscle Trunk	muscle
5	chr1:213150400-213163000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:213151600-213156200	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr1:213151600-213167800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:213151800-213157000	Enhancers	HSMMtube	muscle
9	chr1:213151800-213169400	Weak transcription	Colonic Mucosa	Colon
10	chr1:213152200-213155600	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr1:213152200-213156000	Enhancers	Psoas Muscle	Psoas
12	chr1:213152400-213156000	Genic enhancers	Fetal Stomach	stomach
13	chr1:213152600-213156200	Enhancers	Placenta	Placenta
14	chr1:213152600-213161400	Weak transcription	Fetal Intestine Small	intestine
15	chr1:213152600-213162400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:213152800-213156000	Enhancers	Fetal Heart	heart
17	chr1:213152800-213156200	Enhancers	HSMM	muscle
18	chr1:213153000-213155600	Enhancers	Left Ventricle	heart
19	chr1:213153000-213156200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:213153200-213155600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr1:213153200-213155800	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr1:213153200-213156000	Enhancers	Brain Hippocampus Middle	brain
23	chr1:213153200-213156000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:213153200-213156200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:213153400-213155600	Enhancers	Lung	lung
26	chr1:213153400-213156000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:213153400-213156000	Enhancers	Fetal Thymus	thymus
28	chr1:213153400-213173000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:213153600-213155600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
30	chr1:213153600-213155800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
31	chr1:213153600-213156600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr1:213153600-213163400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:213153800-213168600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr1:213153800-213170200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:213154000-213155600	Genic enhancers	H9 Cell Line	embryonic stem cell
36	chr1:213154000-213156400	Genic enhancers	GM12878-XiMat	blood
37	chr1:213154000-213164600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:213154000-213165000	Weak transcription	Brain Substantia Nigra	brain
39	chr1:213154200-213155600	Enhancers	Gastric	stomach
40	chr1:213154200-213156200	Enhancers	Fetal Brain Male	brain
41	chr1:213154200-213156200	Enhancers	Pancreas	Pancrea
42	chr1:213154200-213167000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:213154400-213155600	Genic enhancers	Fetal Brain Female	brain
44	chr1:213154400-213155600	Enhancers	Thymus	Thymus
45	chr1:213154400-213156000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:213154400-213161000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:213154400-213167600	Weak transcription	Adipose Nuclei	Adipose
48	chr1:213154400-213178200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:213154600-213155600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:213154600-213155600	Enhancers	Esophagus	oesophagus

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