Variant report

Variant	rs6535836
Chromosome Location	chr4:153022292-153022293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM160A1-6	chr4:153021970-153022370	XLOC_003738
2	lnc-FAM160A1-6	chr4:153021970-153022370	ENSG00000245954

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10030518	0.82[EUR][1000 genomes]
rs13140099	0.94[ASN][1000 genomes]
rs13147317	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2406625	0.80[EUR][1000 genomes]
rs61226564	0.82[EUR][1000 genomes]
rs6535837	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535838	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6535839	0.80[EUR][1000 genomes]
rs6535840	0.82[EUR][1000 genomes]
rs6823091	0.82[EUR][1000 genomes]
rs6837375	0.82[EUR][1000 genomes]
rs6843300	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6843947	0.82[EUR][1000 genomes]
rs747110	1.00[CEU][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7668917	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671283	0.80[EUR][1000 genomes]
rs7682568	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv880341	chr4:152861685-153110256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv931416	chr4:152877808-153440553	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6535836	RP11-18H21.1	cis	Whole Blood	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:153014000-153023400	Weak transcription	Fetal Brain Female	brain
2	chr4:153016400-153023600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:153016800-153022800	Weak transcription	Fetal Heart	heart
4	chr4:153017200-153022600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:153017200-153027000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:153018000-153023400	Weak transcription	HSMMtube	muscle
7	chr4:153020000-153025600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr4:153020200-153024000	Enhancers	Primary B cells from peripheral blood	blood
9	chr4:153020200-153024800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:153020200-153025400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr4:153020400-153023400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:153020600-153024200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr4:153020800-153022400	Enhancers	HUVEC	blood vessel
14	chr4:153021000-153023600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:153021000-153025200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr4:153021200-153022400	Enhancers	Left Ventricle	heart
17	chr4:153021200-153022600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr4:153021200-153023000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:153021200-153024200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr4:153021200-153024200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:153021200-153024400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr4:153021200-153024800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr4:153021200-153029400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr4:153021400-153022400	Enhancers	GM12878-XiMat	blood
25	chr4:153021400-153024000	Enhancers	HMEC	breast
26	chr4:153021400-153026200	Enhancers	Spleen	Spleen
27	chr4:153021600-153022400	Enhancers	Brain Anterior Caudate	brain
28	chr4:153021600-153022400	Enhancers	Brain Cingulate Gyrus	brain
29	chr4:153021600-153022400	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr4:153021600-153022400	Enhancers	Fetal Muscle Leg	muscle
31	chr4:153021600-153022400	Enhancers	Lung	lung
32	chr4:153021600-153022600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:153021600-153022800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr4:153021600-153023000	Enhancers	Adipose Nuclei	Adipose
35	chr4:153021600-153023000	Enhancers	Brain Substantia Nigra	brain
36	chr4:153021600-153023000	Enhancers	Esophagus	oesophagus
37	chr4:153021600-153023000	Flanking Active TSS	Dnd41	blood
38	chr4:153021600-153023800	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr4:153021600-153024200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr4:153021600-153024200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:153021600-153024400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:153021600-153024400	Flanking Active TSS	Fetal Thymus	thymus
43	chr4:153021600-153024800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:153021600-153024800	Flanking Active TSS	Thymus	Thymus
45	chr4:153021800-153022400	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr4:153021800-153022400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr4:153021800-153022800	Enhancers	Brain Hippocampus Middle	brain
48	chr4:153021800-153022800	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr4:153021800-153022800	Weak transcription	NH-A	brain
50	chr4:153021800-153024400	Enhancers	NHLF	lung

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