Variant report

Variant	rs1549981
Chromosome Location	chr2:47294762-47294763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47288795..47291567-chr2:47291902..47294947,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CALM2-3	chr2:47294592-47295902	ucscGeneNc_uc002rvu_1

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2570516	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692217	0.85[EUR][1000 genomes]
rs2692218	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2692221	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs919885	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv984437	chr2:47270533-47307361	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv873998	chr2:47273732-47313624	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1549981	PIGF	cis	brain	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47230200-47302800	Strong transcription	Dnd41	blood
2	chr2:47259600-47295000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:47270800-47296600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:47284400-47296400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:47284400-47296400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:47284600-47296000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:47284600-47298400	Strong transcription	Thymus	Thymus
8	chr2:47285000-47295000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:47285000-47295200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:47285000-47295400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:47285200-47295800	Strong transcription	Primary T cells from cord blood	blood
12	chr2:47286400-47295400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:47286600-47295000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:47286800-47296000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr2:47286800-47296600	Strong transcription	Fetal Thymus	thymus
16	chr2:47287400-47296200	Strong transcription	Primary B cells from cord blood	blood
17	chr2:47287800-47296600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr2:47288000-47295000	Genic enhancers	Fetal Muscle Trunk	muscle
19	chr2:47288000-47300400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:47288400-47296400	Enhancers	Fetal Heart	heart
21	chr2:47289600-47295000	Weak transcription	Gastric	stomach
22	chr2:47290200-47295800	Genic enhancers	HepG2	liver
23	chr2:47290400-47299000	Genic enhancers	Fetal Muscle Leg	muscle
24	chr2:47290600-47296400	Genic enhancers	A549	lung
25	chr2:47290800-47297800	Genic enhancers	Primary monocytes fromperipheralblood	blood
26	chr2:47291000-47296200	Genic enhancers	Monocytes-CD14+_RO01746	blood
27	chr2:47291400-47296600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:47291600-47296200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:47291600-47300800	Weak transcription	Brain Germinal Matrix	brain
30	chr2:47291800-47296600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:47291800-47297800	Genic enhancers	Spleen	Spleen
32	chr2:47291800-47301200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr2:47292000-47295000	Weak transcription	Psoas Muscle	Psoas
34	chr2:47292000-47296600	Weak transcription	GM12878-XiMat	blood
35	chr2:47292000-47298800	Enhancers	Placenta	Placenta
36	chr2:47292200-47296400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:47292200-47298200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr2:47292400-47296400	Enhancers	Colon Smooth Muscle	Colon
39	chr2:47292400-47299600	Enhancers	HUVEC	blood vessel
40	chr2:47292600-47302200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:47292800-47295000	Enhancers	Lung	lung
42	chr2:47292800-47296800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr2:47292800-47300000	Enhancers	NHDF-Ad	bronchial
44	chr2:47293000-47296200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr2:47293000-47296200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:47293000-47296400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:47293000-47296600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:47293000-47297400	Weak transcription	Fetal Kidney	kidney
49	chr2:47293000-47300600	Enhancers	Right Ventricle	heart
50	chr2:47293000-47301400	Enhancers	Skeletal Muscle Female	skeletal muscle

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