Variant report

Variant	rs17677601
Chromosome Location	chr2:145223732-145223733
allele	G/T
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	chr2:145221414-145232381	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000176824	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10187371	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10187455	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10187477	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10198698	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10198706	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1060448	0.94[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs12624246	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1365777	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1365779	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17739820	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4662223	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6717029	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs890582	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs890583	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9287359	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv1008032	chr2:144840552-145234229	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17677601	ACVR2A	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:145206800-145253400	Weak transcription	Lung	lung
2	chr2:145211400-145231000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:145215000-145227400	Weak transcription	A549	lung
4	chr2:145215200-145235200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:145216600-145233800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:145217800-145224200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:145217800-145224600	Genic enhancers	K562	blood
8	chr2:145218000-145224400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:145218000-145225200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:145218200-145230200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:145219200-145224400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:145219200-145227400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:145219200-145228200	Weak transcription	HUVEC	blood vessel
14	chr2:145219400-145224000	Enhancers	Brain Substantia Nigra	brain
15	chr2:145219400-145224200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:145219400-145224200	Weak transcription	Aorta	Aorta
17	chr2:145219400-145224200	Enhancers	Brain Anterior Caudate	brain
18	chr2:145219400-145225400	Weak transcription	Spleen	Spleen
19	chr2:145219400-145225600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:145219400-145230000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:145219400-145230200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr2:145219400-145230200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:145219400-145230600	Weak transcription	Psoas Muscle	Psoas
24	chr2:145219400-145232000	Enhancers	Brain Angular Gyrus	brain
25	chr2:145219600-145225400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:145219600-145228000	Enhancers	Brain Cingulate Gyrus	brain
27	chr2:145219600-145228600	Weak transcription	Adipose Nuclei	Adipose
28	chr2:145219600-145230400	Weak transcription	Placenta	Placenta
29	chr2:145219800-145224200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr2:145219800-145224200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:145219800-145224800	Weak transcription	Fetal Stomach	stomach
32	chr2:145220200-145224600	Strong transcription	Primary hematopoietic stem cells	blood
33	chr2:145220200-145226800	Weak transcription	Fetal Kidney	kidney
34	chr2:145220400-145225200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:145220400-145227600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:145220600-145224400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:145220600-145227200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:145220600-145228400	Strong transcription	Primary B cells from cord blood	blood
39	chr2:145220800-145225400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:145220800-145225400	Weak transcription	Fetal Muscle Leg	muscle
41	chr2:145220800-145225400	Weak transcription	Small Intestine	intestine
42	chr2:145220800-145227400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:145220800-145230200	Weak transcription	HSMMtube	muscle
44	chr2:145221000-145224200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:145221200-145224400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:145221200-145225200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:145221200-145230600	Weak transcription	Left Ventricle	heart
48	chr2:145221400-145225200	Weak transcription	NHLF	lung
49	chr2:145221400-145226600	Strong transcription	HSMM	muscle
50	chr2:145221600-145225200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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