Variant report

Variant	rs6535838
Chromosome Location	chr4:153023402-153023403
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13140099	0.94[ASN][1000 genomes]
rs6535836	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6535837	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs747110	0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7668917	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7682568	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6535838	TLR2	cis	parietal	SCAN
rs6535838	RP11-18H21.1	cis	Whole Blood	GTEx
rs6535838	RP11-18H21.1	cis	lung	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:153016400-153023600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:153017200-153027000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:153020000-153025600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr4:153020200-153024000	Enhancers	Primary B cells from peripheral blood	blood
5	chr4:153020200-153024800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:153020200-153025400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr4:153020600-153024200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr4:153021000-153023600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:153021000-153025200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr4:153021200-153024200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr4:153021200-153024200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:153021200-153024400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr4:153021200-153024800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr4:153021200-153029400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr4:153021400-153024000	Enhancers	HMEC	breast
16	chr4:153021400-153026200	Enhancers	Spleen	Spleen
17	chr4:153021600-153023800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr4:153021600-153024200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr4:153021600-153024200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:153021600-153024400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:153021600-153024400	Flanking Active TSS	Fetal Thymus	thymus
22	chr4:153021600-153024800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:153021600-153024800	Flanking Active TSS	Thymus	Thymus
24	chr4:153021800-153024400	Enhancers	NHLF	lung
25	chr4:153021800-153025200	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr4:153022000-153024200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:153022000-153025400	Enhancers	Stomach Mucosa	stomach
28	chr4:153022000-153027000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:153022000-153027200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr4:153022200-153024200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:153022200-153024800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr4:153022200-153026200	Weak transcription	Hela-S3	cervix
33	chr4:153022400-153023600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:153022400-153024400	Enhancers	NHEK	skin
35	chr4:153022400-153024800	Enhancers	Primary hematopoietic stem cells	blood
36	chr4:153022400-153024800	Weak transcription	Brain Anterior Caudate	brain
37	chr4:153022400-153024800	Weak transcription	Fetal Muscle Leg	muscle
38	chr4:153022400-153025800	Enhancers	Primary B cells from cord blood	blood
39	chr4:153022400-153027000	Weak transcription	Left Ventricle	heart
40	chr4:153022400-153027000	Weak transcription	HUVEC	blood vessel
41	chr4:153022400-153027200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr4:153022400-153027200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr4:153022400-153027400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr4:153022400-153027600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr4:153022400-153027600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr4:153022400-153029400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:153022600-153024000	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr4:153022600-153024000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:153022600-153024000	Enhancers	Stomach Smooth Muscle	stomach
50	chr4:153022600-153025200	Weak transcription	Right Ventricle	heart

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