Variant report

Variant	rs11550288
Chromosome Location	chr5:42990975-42990976
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:42988028..42998045-chr5:43036469..43045844,20	K562	blood:
2	chr5:42989723..42997135-chr5:43060250..43070296,19	K562	blood:
3	chr5:42990973..42999044-chr5:43062393..43068169,17	K562	blood:
4	chr5:42989588..43001279-chr5:43004636..43014428,32	K562	blood:
5	chr5:42989969..42995303-chr5:43120044..43124152,6	K562	blood:
6	chr5:42949769..42951285-chr5:42989512..42991530,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C5orf39-2	chr5:42990941-42991008	XLOC_004803
2	lnc-C5orf39-2	chr5:42990941-42991348	XLOC_004803

No data

Variant related genes	Relation type
ENSG00000177738	Chromatin interaction
ENSG00000215068	Chromatin interaction
ENSG00000177721	Chromatin interaction
ENSG00000271788	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000272144	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1084520	1.00[ASN][1000 genomes]
rs13156403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13156729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13158147	1.00[ASN][1000 genomes]
rs13167375	1.00[ASN][1000 genomes]
rs13167991	1.00[ASN][1000 genomes]
rs13170322	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13170959	1.00[ASN][1000 genomes]
rs13171192	1.00[ASN][1000 genomes]
rs13174226	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13175754	1.00[ASN][1000 genomes]
rs13176080	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13180496	1.00[ASN][1000 genomes]
rs13186091	1.00[ASN][1000 genomes]
rs2085100	1.00[ASN][1000 genomes]
rs34157680	1.00[ASN][1000 genomes]
rs34215864	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34345245	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34517361	1.00[ASN][1000 genomes]
rs34735159	1.00[ASN][1000 genomes]
rs34922908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34967469	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35030460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35197809	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35322710	1.00[ASN][1000 genomes]
rs35334781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35484387	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35594379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35756781	1.00[ASN][1000 genomes]
rs36048737	1.00[ASN][1000 genomes]
rs36122053	1.00[ASN][1000 genomes]
rs505573	1.00[ASN][1000 genomes]
rs614386	1.00[ASN][1000 genomes]
rs632730	1.00[ASN][1000 genomes]
rs71627567	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71627568	0.87[AMR][1000 genomes]
rs72746774	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	esv1813779	chr5:42906572-42992040	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
9	nsv1020910	chr5:42929799-43000021	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv537738	chr5:42929799-43000021	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv968169	chr5:42956713-43043472	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	116 gene(s)	inside rSNPs	diseases
12	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
13	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
14	nsv881436	chr5:42967215-43008917	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
15	nsv880447	chr5:42967215-43030798	Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
16	nsv881640	chr5:42978644-43028221	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
17	nsv880415	chr5:42978644-43030798	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11550288	ZNF131	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42985400-42991400	Weak transcription	Placenta	Placenta
2	chr5:42986800-42991200	Weak transcription	NHLF	lung
3	chr5:42987200-42992400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:42988400-42996200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:42988800-42991600	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr5:42988800-42991600	Flanking Active TSS	HUVEC	blood vessel
7	chr5:42988800-42992000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr5:42989000-42991800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr5:42989400-42991000	Enhancers	Adipose Nuclei	Adipose
10	chr5:42989400-42991200	Enhancers	Primary B cells from peripheral blood	blood
11	chr5:42989400-42991800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr5:42989400-42992000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:42989400-42992600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:42989600-42991000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr5:42989800-42991200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:42989800-42991400	Weak transcription	A549	lung
17	chr5:42990000-42991200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:42990000-42991200	Enhancers	Fetal Thymus	thymus
19	chr5:42990000-42991200	Flanking Active TSS	Thymus	Thymus
20	chr5:42990000-42991400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr5:42990000-42991400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr5:42990000-42991400	Enhancers	Spleen	Spleen
23	chr5:42990000-42991600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr5:42990000-42991800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:42990000-42991800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr5:42990000-42991800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:42990200-42991200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr5:42990200-42991200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr5:42990200-42992600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
30	chr5:42990200-42996000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr5:42990400-42991000	Enhancers	Lung	lung
32	chr5:42990600-42991200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:42990600-42991400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr5:42990600-42991600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:42990600-42991600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr5:42990600-42991800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
37	chr5:42990600-42992000	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr5:42990600-42992000	Flanking Active TSS	GM12878-XiMat	blood
39	chr5:42990600-42992600	Flanking Active TSS	K562	blood
40	chr5:42990800-42991000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:42990800-42991000	Bivalent Enhancer	Liver	Liver
42	chr5:42990800-42991000	Bivalent Enhancer	Brain Angular Gyrus	brain
43	chr5:42990800-42991000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
44	chr5:42990800-42991000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
45	chr5:42990800-42991000	Bivalent Enhancer	Left Ventricle	heart
46	chr5:42990800-42991000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
47	chr5:42990800-42991000	Bivalent/Poised TSS	Right Ventricle	heart
48	chr5:42990800-42991000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
49	chr5:42990800-42991000	Flanking Active TSS	NH-A	brain
50	chr5:42990800-42991000	Flanking Active TSS	NHDF-Ad	bronchial

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