Variant report

Variant	rs10963938
Chromosome Location	chr9:19074820-19074821
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10119019	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10511668	0.81[CEU][hapmap]
rs10757023	0.85[CEU][hapmap]
rs10811094	0.80[GIH][hapmap]
rs10811098	0.81[CEU][hapmap];0.80[GIH][hapmap]
rs10963922	0.85[CEU][hapmap];0.85[LWK][hapmap]
rs10963932	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10963935	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10963936	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10963939	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10963948	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10963949	0.82[JPT][hapmap]
rs10963956	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13286328	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13302748	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2095545	0.85[AMR][1000 genomes]
rs2171953	0.83[AMR][1000 genomes]
rs28753724	0.87[AMR][1000 genomes]
rs3824369	0.86[JPT][hapmap];0.83[MEX][hapmap]
rs7022093	0.84[AMR][1000 genomes]
rs7022613	0.87[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7026929	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7031375	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7038917	0.82[AMR][1000 genomes]
rs72696466	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7859319	0.85[AMR][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	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv430003	chr9:19074740-19247826	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10963938	RRAGA	cis	cerebellum	SCAN
rs10963938	IFNB1	cis	cerebellum	SCAN
rs10963938	FAM29A	Cis_1M	lymphoblastoid	RTeQTL
rs10963938	ADFP	cis	multi-tissue	Pritchard
rs10963938	FAM29A	cis	normal skin	skin_eQTL
rs10963938	PLIN2	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19051600-19101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:19051800-19089000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr9:19052000-19075200	Weak transcription	Right Ventricle	heart
4	chr9:19052400-19077000	Weak transcription	Pancreas	Pancrea
5	chr9:19052800-19075600	Weak transcription	Aorta	Aorta
6	chr9:19052800-19092400	Weak transcription	Fetal Brain Male	brain
7	chr9:19054400-19097800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:19054800-19098200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr9:19054800-19100800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:19055600-19082600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:19055600-19091200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr9:19055800-19079800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:19055800-19085200	Strong transcription	Liver	Liver
14	chr9:19055800-19096800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:19055800-19098200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr9:19056000-19086000	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr9:19056000-19091200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr9:19056000-19096400	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr9:19056000-19101200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:19056600-19094800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:19056600-19095200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:19056600-19095400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr9:19056600-19096000	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr9:19056800-19083000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr9:19056800-19096600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr9:19057200-19078200	Strong transcription	Primary B cells from cord blood	blood
27	chr9:19057400-19075800	Weak transcription	Gastric	stomach
28	chr9:19057600-19077000	Weak transcription	Esophagus	oesophagus
29	chr9:19060400-19076800	Weak transcription	Brain Substantia Nigra	brain
30	chr9:19061200-19076800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:19062000-19102200	Weak transcription	Stomach Mucosa	stomach
32	chr9:19062800-19079000	Weak transcription	NHLF	lung
33	chr9:19063000-19077000	Weak transcription	Brain Angular Gyrus	brain
34	chr9:19063200-19077000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr9:19066200-19077400	Strong transcription	Dnd41	blood
36	chr9:19066400-19083400	Strong transcription	Placenta	Placenta
37	chr9:19066400-19085600	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr9:19066400-19096600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr9:19066800-19100400	Weak transcription	Fetal Heart	heart
40	chr9:19066800-19100800	Weak transcription	Small Intestine	intestine
41	chr9:19067000-19078400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:19067000-19084800	Weak transcription	Colonic Mucosa	Colon
43	chr9:19067400-19086600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr9:19068000-19077600	Strong transcription	A549	lung
45	chr9:19068800-19075000	Strong transcription	Primary hematopoietic stem cells	blood
46	chr9:19068800-19079800	Strong transcription	Fetal Muscle Leg	muscle
47	chr9:19068800-19085400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:19068800-19096800	Strong transcription	Fetal Thymus	thymus
49	chr9:19069800-19076800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:19069800-19080800	Strong transcription	Fetal Lung	lung

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