Variant report

Variant	rs3954044
Chromosome Location	chr10:49683566-49683567
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:49683409..49685423-chr10:49724678..49727528,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10857574	0.81[ASN][1000 genomes]
rs11101333	0.82[ASN][1000 genomes]
rs11101336	0.83[ASN][1000 genomes]
rs11101340	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11598657	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1867579	0.89[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2166224	0.86[EUR][1000 genomes]
rs2377354	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs3844600	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs3853762	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3888299	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3888909	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3889334	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3896665	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4838594	0.84[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs4838597	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4838598	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61838750	0.85[EUR][1000 genomes]
rs730509	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[ASN][1000 genomes]
rs9794032	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv467191	chr10:49669142-49735563	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv550813	chr10:49669142-49735563	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3954044	ARHGAP22	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49678200-49687200	Weak transcription	HSMMtube	muscle
2	chr10:49678400-49683800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr10:49678800-49684000	Weak transcription	Placenta	Placenta
4	chr10:49678800-49684200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr10:49678800-49684200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr10:49678800-49684200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr10:49678800-49684200	Weak transcription	Right Atrium	heart
8	chr10:49679000-49683800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr10:49679000-49683800	Weak transcription	Fetal Stomach	stomach
10	chr10:49679000-49684200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr10:49679000-49684400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr10:49679200-49690400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr10:49679400-49684000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr10:49679400-49686200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr10:49679600-49683800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr10:49679600-49684000	Weak transcription	Ovary	ovary
17	chr10:49679600-49685400	Weak transcription	Brain Angular Gyrus	brain
18	chr10:49679800-49684000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr10:49679800-49684000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr10:49679800-49684200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr10:49679800-49684200	Weak transcription	Fetal Thymus	thymus
22	chr10:49679800-49684600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr10:49679800-49686800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr10:49679800-49689000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr10:49679800-49704200	Weak transcription	NH-A	brain
26	chr10:49679800-49704200	Weak transcription	NHDF-Ad	bronchial
27	chr10:49680000-49684200	Weak transcription	Esophagus	oesophagus
28	chr10:49680000-49684400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr10:49680200-49684400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr10:49680200-49684600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr10:49680400-49684600	Weak transcription	NHEK	skin
32	chr10:49680800-49684000	Weak transcription	HMEC	breast
33	chr10:49681000-49684200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr10:49681200-49689200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr10:49681400-49683800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr10:49681600-49684000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr10:49681800-49684600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr10:49682200-49684000	Weak transcription	Osteobl	bone
39	chr10:49682600-49684600	Weak transcription	HSMM	muscle
40	chr10:49682800-49685400	Enhancers	Primary hematopoietic stem cells	blood
41	chr10:49683000-49686200	Enhancers	K562	blood
42	chr10:49683200-49684200	Weak transcription	HUVEC	blood vessel
43	chr10:49683200-49687600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr10:49683400-49683600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr10:49683400-49683600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr10:49683400-49684000	Enhancers	Brain Substantia Nigra	brain
47	chr10:49683400-49684000	Active TSS	Spleen	Spleen
48	chr10:49683400-49684400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr10:49683400-49684800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr10:49683400-49689200	Strong transcription	NHLF	lung

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