Variant report

Variant	rs3010780
Chromosome Location	chr1:213164918-213164919
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:213164045..213166844-chr1:213187176..213189622,2	K562	blood:
2	chr1:213151581..213154510-chr1:213163041..213165443,2	MCF-7	breast:
3	chr1:213164117..213166257-chr1:213181504..213183921,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VASH2-1	chr1:213164893-213165379	NONHSAT009416

Variant related genes	Relation type
ENSG00000174606	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10465694	0.83[ASN][1000 genomes]
rs1976333	0.83[ASN][1000 genomes]
rs2132428	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2172982	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2935209	0.92[ASN][1000 genomes]
rs2935219	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2936011	0.90[ASN][1000 genomes]
rs3002285	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3010779	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	0.84[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3010789	0.93[ASN][1000 genomes]
rs3124668	0.84[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3738805	0.84[JPT][hapmap]
rs4543872	0.94[ASN][1000 genomes]
rs4951475	0.91[ASN][1000 genomes]
rs4951476	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.83[ASN][1000 genomes]
rs4951479	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4951662	1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs6657234	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6671872	1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs6691488	0.95[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs6692144	1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[MKK][hapmap];0.83[YRI][hapmap]
rs6699158	0.80[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3010780	BATF3	cis	parietal	SCAN
rs3010780	ANGEL2	cis	cerebellum	SCAN
rs3010780	ANGEL2	cis	parietal	SCAN

Chromatin state (count:123 , 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	chr1:213151600-213167800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:213151800-213169400	Weak transcription	Colonic Mucosa	Colon
4	chr1:213153400-213173000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:213153800-213168600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:213153800-213170200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:213154000-213165000	Weak transcription	Brain Substantia Nigra	brain
8	chr1:213154200-213167000	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:213154400-213167600	Weak transcription	Adipose Nuclei	Adipose
10	chr1:213154400-213178200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:213154600-213170200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:213154600-213187400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:213154800-213167600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:213154800-213177400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:213154800-213178200	Weak transcription	Brain Angular Gyrus	brain
16	chr1:213154800-213188000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:213154800-213188400	Weak transcription	Spleen	Spleen
18	chr1:213155000-213168400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:213155200-213165200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:213155200-213177800	Weak transcription	Right Ventricle	heart
21	chr1:213155400-213165400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr1:213155400-213166400	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr1:213155400-213178400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:213155600-213166400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:213155600-213168200	Weak transcription	Thymus	Thymus
26	chr1:213155600-213168800	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:213155600-213169400	Weak transcription	Lung	lung
28	chr1:213155600-213178400	Weak transcription	Gastric	stomach
29	chr1:213155600-213188000	Weak transcription	Aorta	Aorta
30	chr1:213155600-213188000	Weak transcription	Esophagus	oesophagus
31	chr1:213155800-213168400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:213156000-213168800	Weak transcription	Right Atrium	heart
33	chr1:213156000-213176800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:213156000-213177200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:213156200-213165000	Weak transcription	Placenta	Placenta
36	chr1:213156200-213165200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:213156200-213168200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:213156200-213168600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:213156200-213187400	Weak transcription	Fetal Brain Male	brain
40	chr1:213156200-213188000	Weak transcription	Pancreas	Pancrea
41	chr1:213156400-213170000	Weak transcription	Brain Anterior Caudate	brain
42	chr1:213156600-213170400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:213156600-213176600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:213157200-213178400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr1:213158400-213188000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:213158800-213169200	Weak transcription	Fetal Stomach	stomach
47	chr1:213160000-213165200	Weak transcription	Primary B cells from cord blood	blood
48	chr1:213160200-213188000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:213160400-213165400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:213160400-213167400	Weak transcription	Rectal Mucosa Donor 31	rectum

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