Variant report

Variant	rs61061894
Chromosome Location	chr1:173430449-173430450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC9A11-1	chr1:173429517-173430501	ENSG00000203739.3
2	lnc-SLC9A11-1	chr1:173430332-173430501	NONHSAT007636

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11800778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809166	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811598	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12075952	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12085083	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12562415	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34035460	0.89[AFR][1000 genomes]
rs34619706	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35128709	0.89[AFR][1000 genomes]
rs35263596	0.90[ASN][1000 genomes]
rs3934577	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55741047	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55816799	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57231379	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57262055	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57951216	0.89[ASN][1000 genomes]
rs59834293	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60302114	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60587131	0.90[ASN][1000 genomes]
rs60969203	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61261546	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6700269	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6700499	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6702339	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72726915	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72726936	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72726946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72726948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72726949	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74126390	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7534736	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7555324	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831915	chr1:173268424-173482157	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61061894	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173419000-173432000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:173419000-173439000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:173421000-173432200	Weak transcription	Fetal Brain Male	brain
4	chr1:173421400-173434000	Weak transcription	Psoas Muscle	Psoas
5	chr1:173423200-173432000	Weak transcription	A549	lung
6	chr1:173423400-173432600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:173423600-173432600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:173423800-173433400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:173423800-173436600	Weak transcription	NHDF-Ad	bronchial
10	chr1:173423800-173442400	Weak transcription	NH-A	brain
11	chr1:173424400-173430600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:173425200-173442400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:173425400-173432200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:173426000-173431400	Weak transcription	Fetal Kidney	kidney
15	chr1:173427600-173431200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr1:173428600-173431000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:173428600-173431600	Strong transcription	Liver	Liver
18	chr1:173428800-173430800	Strong transcription	Fetal Brain Female	brain
19	chr1:173428800-173430800	Strong transcription	Fetal Stomach	stomach
20	chr1:173428800-173431000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:173428800-173431000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:173428800-173431000	Strong transcription	Brain Hippocampus Middle	brain
23	chr1:173428800-173431000	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr1:173428800-173431200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:173428800-173431200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:173428800-173431400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:173428800-173431400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:173428800-173431400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:173428800-173431400	Strong transcription	Brain Anterior Caudate	brain
30	chr1:173428800-173432000	Strong transcription	Primary T cells from cord blood	blood
31	chr1:173429000-173430600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:173429000-173430600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:173429000-173430600	Strong transcription	Fetal Intestine Small	intestine
34	chr1:173429000-173430600	Strong transcription	Rectal Smooth Muscle	rectum
35	chr1:173429000-173430800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:173429000-173430800	Strong transcription	Lung	lung
37	chr1:173429000-173430800	Strong transcription	Thymus	Thymus
38	chr1:173429000-173431000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:173429000-173431000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:173429000-173431000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:173429000-173431000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:173429000-173431000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:173429000-173431000	Strong transcription	Adipose Nuclei	Adipose
44	chr1:173429000-173431000	Strong transcription	Brain Cingulate Gyrus	brain
45	chr1:173429000-173431000	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr1:173429000-173431000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:173429000-173431000	Strong transcription	Left Ventricle	heart
48	chr1:173429000-173431000	Strong transcription	Ovary	ovary
49	chr1:173429000-173431000	Transcr. at gene 5' and 3'	HSMMtube	muscle
50	chr1:173429000-173431000	Strong transcription	Osteobl	bone

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