Variant report

Variant	rs3010787
Chromosome Location	chr1:213180791-213180792
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:213179534..213181909-chr1:213222762..213224304,2	K562	blood:
2	chr1:213180453..213182672-chr1:213253594..213256441,2	K562	blood:
3	chr1:213180724..213183170-chr1:213240316..213242506,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10465694	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10864034	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1566247	0.81[AMR][1000 genomes]
rs1976333	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1995151	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]
rs2132428	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2172982	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2935209	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2935219	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936010	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2936011	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3002284	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs3002285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3010779	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]
rs3010780	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	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3123307	0.82[EUR][1000 genomes]
rs3124668	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738805	0.84[JPT][hapmap]
rs4543872	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4951475	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4951476	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4951479	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4951662	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs6540778	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6657234	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6666814	0.80[AFR][1000 genomes]
rs6671872	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs6691488	0.84[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6692144	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap]
rs6699158	0.85[AMR][1000 genomes];0.83[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3010787	LOC148696	cis	cerebellum	SCAN
rs3010787	RPS6KC1	cis	Artery Tibial	GTEx
rs3010787	BATF3	cis	parietal	SCAN
rs3010787	ANGEL2	cis	parietal	SCAN
rs3010787	ANGEL2	cis	cerebellum	SCAN
rs3010787	ANGEL2	cis	Esophagus Mucosa	GTEx
rs3010787	KCNH1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213154600-213187400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:213154800-213188000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:213154800-213188400	Weak transcription	Spleen	Spleen
4	chr1:213155600-213188000	Weak transcription	Aorta	Aorta
5	chr1:213155600-213188000	Weak transcription	Esophagus	oesophagus
6	chr1:213156200-213187400	Weak transcription	Fetal Brain Male	brain
7	chr1:213156200-213188000	Weak transcription	Pancreas	Pancrea
8	chr1:213158400-213188000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:213160200-213188000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:213160400-213187200	Weak transcription	NHLF	lung
11	chr1:213162000-213184600	Weak transcription	Psoas Muscle	Psoas
12	chr1:213162200-213188000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:213162800-213181200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:213162800-213183000	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr1:213163200-213187400	Weak transcription	Stomach Mucosa	stomach
16	chr1:213165400-213181600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:213166000-213182200	Strong transcription	Fetal Intestine Large	intestine
18	chr1:213166000-213184200	Weak transcription	HepG2	liver
19	chr1:213167000-213181000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:213167600-213182600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:213167800-213187000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:213167800-213187000	Weak transcription	Fetal Heart	heart
23	chr1:213167800-213187800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:213168200-213181800	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:213168600-213183000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:213169000-213182600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:213169000-213186800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:213169000-213187200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:213169000-213187800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:213169800-213186400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:213170000-213188000	Weak transcription	Colonic Mucosa	Colon
32	chr1:213170600-213187800	Weak transcription	Fetal Kidney	kidney
33	chr1:213172400-213181800	Strong transcription	Fetal Thymus	thymus
34	chr1:213172600-213182800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:213172800-213180800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:213172800-213181400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:213172800-213182600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:213173000-213180800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:213173000-213182000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr1:213173000-213182400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:213173000-213183000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:213173000-213183400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:213173000-213186800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr1:213173000-213187000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:213173200-213182000	Strong transcription	Liver	Liver
46	chr1:213173200-213183000	Strong transcription	Dnd41	blood
47	chr1:213173400-213182200	Strong transcription	Primary B cells from cord blood	blood
48	chr1:213173600-213182200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr1:213174600-213181000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr1:213174800-213181200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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