Variant report

Variant	rs3010779
Chromosome Location	chr1:213162146-213162147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:213161145-213162162	Hela-S3	cervix:	n/a	n/a
2	STAT3	chr1:213162023-213162564	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:213161598-213162309	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:213161546-213164134	K562	blood:	n/a	n/a
5	POLR2A	chr1:213160941-213162452	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:213133878..213135419-chr1:213160390..213162538,2	MCF-7	breast:
2	chr1:213155649..213157570-chr1:213160217..213162394,2	MCF-7	breast:

Variant related genes	Relation type
VASH2	TF binding region
ENSG00000143494	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10465694	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10864034	0.83[AMR][1000 genomes]
rs1566247	0.83[AMR][1000 genomes]
rs1976333	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2132428	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs2172982	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2935209	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2935219	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2936010	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2936011	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002284	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs3002285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3010780	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3010787	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3010789	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3123307	0.83[EUR][1000 genomes]
rs3124668	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3738805	0.90[JPT][hapmap]
rs4543872	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4951475	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4951476	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4951479	0.82[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes]
rs4951662	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs6540778	0.82[AMR][1000 genomes]
rs6540780	0.81[AMR][1000 genomes]
rs6657234	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs6658259	0.81[AMR][1000 genomes]
rs6666814	0.82[AMR][1000 genomes]
rs6671872	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.90[TSI][hapmap]
rs6691488	0.95[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs6692056	0.81[AMR][1000 genomes]
rs6692144	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];0.90[TSI][hapmap]
rs6699158	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3010779	ANGEL2	cis	Esophagus Mucosa	GTEx
rs3010779	LOC148696	cis	cerebellum	SCAN
rs3010779	RPS6KC1	cis	Artery Tibial	GTEx
rs3010779	ANGEL2	cis	cerebellum	SCAN
rs3010779	ANGEL2	cis	parietal	SCAN
rs3010779	BATF3	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213148400-213165400	Weak transcription	Fetal Kidney	kidney
2	chr1:213150400-213163000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:213151600-213167800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:213151800-213169400	Weak transcription	Colonic Mucosa	Colon
5	chr1:213152600-213162400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:213153400-213173000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:213153600-213163400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:213153800-213168600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:213153800-213170200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:213154000-213164600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:213154000-213165000	Weak transcription	Brain Substantia Nigra	brain
12	chr1:213154200-213167000	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:213154400-213167600	Weak transcription	Adipose Nuclei	Adipose
14	chr1:213154400-213178200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:213154600-213170200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:213154600-213187400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:213154800-213167600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:213154800-213177400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:213154800-213178200	Weak transcription	Brain Angular Gyrus	brain
20	chr1:213154800-213188000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:213154800-213188400	Weak transcription	Spleen	Spleen
22	chr1:213155000-213168400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:213155200-213163000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:213155200-213165200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr1:213155200-213177800	Weak transcription	Right Ventricle	heart
26	chr1:213155400-213163000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:213155400-213163200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:213155400-213165400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr1:213155400-213166400	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr1:213155400-213178400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:213155600-213162200	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr1:213155600-213162800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:213155600-213162800	Weak transcription	Left Ventricle	heart
34	chr1:213155600-213166400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:213155600-213168200	Weak transcription	Thymus	Thymus
36	chr1:213155600-213168800	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:213155600-213169400	Weak transcription	Lung	lung
38	chr1:213155600-213178400	Weak transcription	Gastric	stomach
39	chr1:213155600-213188000	Weak transcription	Aorta	Aorta
40	chr1:213155600-213188000	Weak transcription	Esophagus	oesophagus
41	chr1:213155800-213168400	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:213156000-213162800	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:213156000-213168800	Weak transcription	Right Atrium	heart
44	chr1:213156000-213176800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:213156000-213177200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:213156200-213165000	Weak transcription	Placenta	Placenta
47	chr1:213156200-213165200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:213156200-213168200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:213156200-213168600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:213156200-213187400	Weak transcription	Fetal Brain Male	brain

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