Variant report

Variant	rs1060448
Chromosome Location	chr2:145251094-145251095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:145232088..145234387-chr2:145250411..145252365,2	K562	blood:
2	chr2:145088317..145091113-chr2:145250622..145252280,2	MCF-7	breast:
3	chr2:145250390..145252682-chr2:145338354..145340585,2	K562	blood:

Variant related genes	Relation type
ENSG00000121964	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10187371	0.92[EUR][1000 genomes]
rs10187455	0.94[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs10187477	0.94[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10198698	0.94[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs10198706	0.93[EUR][1000 genomes]
rs12624246	0.94[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs1365777	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs1365779	0.94[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs17677601	0.94[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs17739820	0.94[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4662223	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs6717029	0.94[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs72992185	0.85[ASN][1000 genomes]
rs7564464	0.81[YRI][hapmap]
rs7598023	0.80[EUR][1000 genomes]
rs890582	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs890583	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs9287359	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532755	chr2:144631279-145270874	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1006344	chr2:144657716-145334899	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv535951	chr2:144657716-145334899	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1067624	chr2:144657717-145425705	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv531413	chr2:144657717-145425705	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv532756	chr2:144746353-145315596	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv997624	chr2:144906679-145294503	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv535952	chr2:144906679-145294503	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv532757	chr2:144922143-145263446	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
10	nsv916172	chr2:144970681-145425713	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv948474	chr2:145035890-145436665	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv535953	chr2:145099512-145336083	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv535954	chr2:145128008-145311097	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
14	nsv535955	chr2:145143961-145298714	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
15	nsv535956	chr2:145178224-145311097	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
16	nsv1002563	chr2:145182201-145863253	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
17	nsv535957	chr2:145182201-145863253	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
18	nsv535958	chr2:145190081-145285400	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
19	nsv531662	chr2:145219415-145422833	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
20	nsv535959	chr2:145228576-145285400	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	n/a
21	nsv535960	chr2:145228576-145294503	Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	n/a
22	nsv535961	chr2:145234169-145285400	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	n/a
23	nsv535962	chr2:145250117-145294503	Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1060448	ACVR2A	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:145206800-145253400	Weak transcription	Lung	lung
2	chr2:145229000-145253600	Weak transcription	HUVEC	blood vessel
3	chr2:145234200-145252600	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:145237600-145263000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:145238200-145262000	Weak transcription	NH-A	brain
6	chr2:145240000-145263000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:145242200-145252600	Weak transcription	Aorta	Aorta
8	chr2:145242400-145253000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:145242400-145253200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:145242400-145253200	Weak transcription	Psoas Muscle	Psoas
11	chr2:145242400-145254600	Weak transcription	Right Ventricle	heart
12	chr2:145242600-145252200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:145243200-145252000	Enhancers	Brain Angular Gyrus	brain
14	chr2:145243200-145253400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:145245800-145253200	Weak transcription	Left Ventricle	heart
16	chr2:145245800-145254400	Weak transcription	Small Intestine	intestine
17	chr2:145246800-145251400	Genic enhancers	K562	blood
18	chr2:145246800-145267800	Genic enhancers	Primary monocytes fromperipheralblood	blood
19	chr2:145247400-145251200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:145247400-145251600	Strong transcription	Fetal Muscle Leg	muscle
21	chr2:145247400-145253200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:145247400-145255800	Weak transcription	Gastric	stomach
23	chr2:145247600-145251400	Strong transcription	Adipose Nuclei	Adipose
24	chr2:145247600-145252200	Weak transcription	Ovary	ovary
25	chr2:145247600-145252200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:145247600-145252200	Weak transcription	Right Atrium	heart
27	chr2:145247600-145253200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:145247600-145253400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:145247600-145268000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:145247800-145252800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:145247800-145252800	Weak transcription	Fetal Kidney	kidney
32	chr2:145248000-145251200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr2:145248200-145252200	Genic enhancers	Monocytes-CD14+_RO01746	blood
34	chr2:145248400-145251400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:145248400-145252000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr2:145248400-145252400	Enhancers	Fetal Brain Male	brain
37	chr2:145248800-145251800	Weak transcription	Fetal Brain Female	brain
38	chr2:145248800-145252000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:145248800-145252200	Enhancers	Brain Hippocampus Middle	brain
40	chr2:145248800-145252200	Weak transcription	Fetal Stomach	stomach
41	chr2:145248800-145252200	Weak transcription	HSMMtube	muscle
42	chr2:145248800-145253000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:145248800-145254400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:145248800-145254400	Enhancers	Brain Substantia Nigra	brain
45	chr2:145248800-145254600	Weak transcription	Placenta	Placenta
46	chr2:145248800-145255200	Weak transcription	Esophagus	oesophagus
47	chr2:145249200-145251400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:145249400-145252000	Strong transcription	HSMM	muscle
49	chr2:145249400-145253000	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr2:145249400-145255000	Enhancers	Fetal Heart	heart

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