Variant report

Variant	rs10928390
Chromosome Location	chr2:149011941-149011942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10206569	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210377	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10432369	0.82[ASN][1000 genomes]
rs10928388	0.96[ASN][1000 genomes]
rs10928389	0.99[ASN][1000 genomes]
rs1120671	0.98[ASN][1000 genomes]
rs11676308	0.86[ASN][1000 genomes]
rs11685302	0.96[ASN][1000 genomes]
rs11692246	0.86[ASN][1000 genomes]
rs12691780	0.96[ASN][1000 genomes]
rs12691781	0.96[ASN][1000 genomes]
rs13001946	0.82[ASN][1000 genomes]
rs13022005	0.82[ASN][1000 genomes]
rs13027785	0.99[ASN][1000 genomes]
rs13032996	0.84[ASN][1000 genomes]
rs13392141	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425594	1.00[ASN][1000 genomes]
rs1449960	0.93[ASN][1000 genomes]
rs1453318	0.91[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs17274896	0.86[ASN][1000 genomes]
rs2044760	0.93[ASN][1000 genomes]
rs2044761	0.93[ASN][1000 genomes]
rs2084954	0.86[ASN][1000 genomes]
rs2167127	0.96[ASN][1000 genomes]
rs2839755	0.82[ASN][1000 genomes]
rs2890917	0.98[ASN][1000 genomes]
rs35042809	0.84[ASN][1000 genomes]
rs35749985	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4972276	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4972338	0.85[ASN][1000 genomes]
rs4972341	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972343	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6430305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[ASN][1000 genomes]
rs6721794	0.96[ASN][1000 genomes]
rs6746932	0.86[ASN][1000 genomes]
rs7565035	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7570104	0.96[ASN][1000 genomes]
rs7572948	0.82[ASN][1000 genomes]
rs961207	0.96[ASN][1000 genomes]
rs991554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001339	chr2:148755022-149020866	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv535977	chr2:148755022-149020866	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv869146	chr2:148787051-149060763	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1004431	chr2:148859099-149054114	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1009608	chr2:148897348-149133718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv2753542	chr2:149004714-149268503	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10928390	ACVR2A	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148994800-149016600	Weak transcription	Fetal Brain Male	brain
2	chr2:148995000-149019800	Weak transcription	Aorta	Aorta
3	chr2:148995000-149030800	Weak transcription	Left Ventricle	heart
4	chr2:148995400-149013400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:148995400-149015200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:148996400-149030400	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:148997000-149012000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:148999400-149016400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:149002600-149015600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:149002800-149012000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:149002800-149012000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:149002800-149016600	Weak transcription	NHLF	lung
13	chr2:149008000-149013800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:149009200-149016600	ZNF genes & repeats	GM12878-XiMat	blood
15	chr2:149009400-149012200	ZNF genes & repeats	Primary T cells from cord blood	blood
16	chr2:149009400-149017600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:149009600-149012000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
18	chr2:149009600-149017600	ZNF genes & repeats	Fetal Intestine Small	intestine
19	chr2:149010000-149012400	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
20	chr2:149010400-149012400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
21	chr2:149010400-149013600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:149010600-149013000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:149010800-149012200	ZNF genes & repeats	Fetal Lung	lung
24	chr2:149010800-149012400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr2:149010800-149012800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
26	chr2:149010800-149013400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:149010800-149013400	Weak transcription	HSMM	muscle
28	chr2:149010800-149014800	ZNF genes & repeats	Dnd41	blood
29	chr2:149011000-149012000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:149011000-149012200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:149011000-149012200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
32	chr2:149011000-149012600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:149011000-149013600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
34	chr2:149011000-149014400	ZNF genes & repeats	Fetal Stomach	stomach
35	chr2:149011000-149017000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:149011200-149012200	Weak transcription	Brain Anterior Caudate	brain
37	chr2:149011200-149012400	ZNF genes & repeats	Ovary	ovary
38	chr2:149011200-149012600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:149011200-149012600	ZNF genes & repeats	Pancreas	Pancrea
40	chr2:149011200-149012800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:149011200-149013600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
42	chr2:149011200-149014200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
43	chr2:149011200-149014400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr2:149011400-149012000	ZNF genes & repeats	Placenta	Placenta
45	chr2:149011400-149012200	Strong transcription	Rectal Smooth Muscle	rectum
46	chr2:149011400-149012400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
47	chr2:149011400-149012800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:149011400-149013000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:149011400-149013000	Strong transcription	Right Ventricle	heart
50	chr2:149011400-149013200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived

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