Variant report

Variant	rs2377698
Chromosome Location	chr10:51128148-51128149
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10508917	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11592062	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11598461	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11598949	0.80[AFR][1000 genomes]
rs11599492	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11813858	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12774346	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17719813	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17719843	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17719866	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17776131	0.82[AMR][1000 genomes]
rs34419748	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34714687	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35547965	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs3877001	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4012652	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4285799	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4495813	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4592357	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838566	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4838568	0.86[AMR][1000 genomes]
rs4838573	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838575	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5013289	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61846915	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61846922	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61846925	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61846931	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7067802	0.82[AMR][1000 genomes]
rs7093312	0.80[EUR][1000 genomes]
rs7921218	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[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	esv2758219	chr10:50971974-51925166	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	esv2759749	chr10:50971974-51925166	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv428232	chr10:50971974-51925166	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv895379	chr10:51022933-51187793	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv32940	chr10:51051718-51488059	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv895381	chr10:51094660-51515534	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2377698	AGAP6	cis	Nerve Tibial	GTEx
rs2377698	AGAP6	cis	lung	GTEx
rs2377698	AGAP6	cis	Artery Tibial	GTEx
rs2377698	AGAP6	cis	Skin Sun Exposed Lower leg	GTEx
rs2377698	AGAP6	cis	Esophagus Muscularis	GTEx
rs2377698	CTGLF3	cis	multi-tissue	Pritchard
rs2377698	AGAP6	cis	Thyroid	GTEx
rs2377698	AGAP6	cis	Adipose Subcutaneous	GTEx
rs2377698	AGAP6	cis	Whole Blood	GTEx
rs2377698	AGAP6	cis	Muscle Skeletal	GTEx
rs2377698	AGAP6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:51080800-51130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:51084400-51131800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr10:51084600-51130200	Weak transcription	Fetal Lung	lung
4	chr10:51084600-51136000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr10:51084600-51136600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr10:51084600-51137800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr10:51085400-51138200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr10:51085400-51138600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr10:51087000-51132000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr10:51091200-51138000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:51095000-51137200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr10:51100800-51137600	Weak transcription	Lung	lung
13	chr10:51102000-51138000	Weak transcription	Spleen	Spleen
14	chr10:51103800-51138000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr10:51108600-51129600	Weak transcription	HSMMtube	muscle
16	chr10:51108800-51137400	Weak transcription	Ovary	ovary
17	chr10:51109000-51138200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr10:51110000-51137600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr10:51110400-51137400	Weak transcription	Thymus	Thymus
20	chr10:51111200-51136200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr10:51111400-51130200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr10:51111400-51131400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr10:51111800-51137600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr10:51112200-51137800	Weak transcription	Colon Smooth Muscle	Colon
25	chr10:51113400-51130800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr10:51116000-51136400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr10:51116200-51137600	Weak transcription	Fetal Muscle Leg	muscle
28	chr10:51116400-51137600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr10:51116600-51134400	Weak transcription	HepG2	liver
30	chr10:51116600-51135800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr10:51116600-51137600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr10:51117000-51136200	Weak transcription	A549	lung
33	chr10:51117000-51136600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr10:51117200-51131800	Weak transcription	Osteobl	bone
35	chr10:51117600-51136800	Weak transcription	Left Ventricle	heart
36	chr10:51118800-51137400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr10:51119200-51134600	Weak transcription	Gastric	stomach
38	chr10:51119200-51138400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr10:51119400-51130000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr10:51119400-51130000	Weak transcription	Fetal Thymus	thymus
41	chr10:51119400-51136000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr10:51119600-51130200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr10:51119600-51137600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr10:51119600-51137600	Weak transcription	NH-A	brain
45	chr10:51120600-51130000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr10:51120600-51131800	Weak transcription	HUVEC	blood vessel
47	chr10:51120600-51137600	Weak transcription	HSMM	muscle
48	chr10:51120800-51132000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr10:51121000-51136000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr10:51121200-51132800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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