Variant report

Variant	rs7990988
Chromosome Location	chr13:50100782-50100783
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1046027	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1046028	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1046295	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1062979	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12146924	0.91[JPT][hapmap]
rs12429813	0.82[CEU][hapmap]
rs17073051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1925742	0.95[JPT][hapmap];0.82[YRI][hapmap]
rs2038881	0.86[JPT][hapmap]
rs2980	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3033	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3186012	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3186013	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3186024	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36075670	0.83[EUR][1000 genomes]
rs3765526	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3829366	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4340215	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs4430650	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs4941643	0.81[CEU][hapmap]
rs4942833	0.92[CEU][hapmap]
rs4942836	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4942838	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4942839	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4942840	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4942843	0.95[JPT][hapmap]
rs6561533	0.93[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap]
rs6561534	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6561538	0.83[EUR][1000 genomes]
rs67307832	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7139494	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7317772	0.80[CEU][hapmap]
rs7317982	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7322077	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7322908	0.91[ASN][1000 genomes]
rs7323493	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7323716	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7331262	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7331330	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7333969	0.90[JPT][hapmap]
rs7337718	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7339167	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7988427	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7989504	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7991031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7991264	0.83[ASN][1000 genomes]
rs7995684	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7996994	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7997737	0.81[CEU][hapmap]
rs9316454	0.81[CEU][hapmap]
rs942870	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9526565	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9526566	0.81[EUR][1000 genomes]
rs9526567	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9526568	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535254	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535255	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535256	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535257	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535258	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[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	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking 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	9 gene(s)	inside rSNPs	diseases
4	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7990988	CAB39L	Cis_1M	lymphoblastoid	RTeQTL
rs7990988	PHF11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50075000-50102400	Weak transcription	NH-A	brain
2	chr13:50075000-50143800	Weak transcription	Small Intestine	intestine
3	chr13:50077600-50114000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr13:50080000-50107000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr13:50080200-50104600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr13:50080600-50101000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr13:50080600-50104600	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr13:50083600-50103600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr13:50084000-50104800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr13:50084800-50104200	Strong transcription	GM12878-XiMat	blood
11	chr13:50085400-50104800	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr13:50086400-50113600	Weak transcription	Brain Angular Gyrus	brain
13	chr13:50086600-50101600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr13:50086600-50103200	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr13:50086600-50106200	Strong transcription	Fetal Thymus	thymus
16	chr13:50086600-50108800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr13:50086600-50114200	Weak transcription	Fetal Brain Female	brain
18	chr13:50086800-50101600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr13:50087800-50103600	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr13:50088200-50113600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr13:50088400-50151000	Weak transcription	Psoas Muscle	Psoas
22	chr13:50088600-50134200	Weak transcription	Stomach Mucosa	stomach
23	chr13:50089200-50107400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr13:50089400-50114200	Weak transcription	Colon Smooth Muscle	Colon
25	chr13:50089800-50101200	Weak transcription	NHEK	skin
26	chr13:50090000-50101200	Weak transcription	Left Ventricle	heart
27	chr13:50090000-50113600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr13:50090000-50122800	Weak transcription	Ovary	ovary
29	chr13:50090000-50123600	Weak transcription	Esophagus	oesophagus
30	chr13:50090200-50101000	Weak transcription	Brain Anterior Caudate	brain
31	chr13:50090200-50101200	Weak transcription	Brain Substantia Nigra	brain
32	chr13:50090200-50114200	Weak transcription	Aorta	Aorta
33	chr13:50090200-50117800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr13:50090400-50106600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr13:50090400-50113400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr13:50090400-50114200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr13:50090800-50104200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr13:50091000-50104000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr13:50091000-50114200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr13:50091400-50138800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr13:50091800-50107600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr13:50092000-50101200	Strong transcription	NHDF-Ad	bronchial
43	chr13:50092000-50102200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr13:50092000-50108000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr13:50092000-50112200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr13:50092000-50114200	Weak transcription	Fetal Brain Male	brain
47	chr13:50092200-50105400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr13:50092200-50105800	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr13:50092200-50113400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr13:50093000-50108000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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