Variant report

Variant	rs55893855
Chromosome Location	chr10:46162374-46162375
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10900228	1.00[AFR][1000 genomes]
rs11239580	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11239583	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11492889	1.00[AFR][1000 genomes]
rs34257967	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55654107	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55895325	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61854124	1.00[AFR][1000 genomes]
rs61854126	0.92[AMR][1000 genomes];0.82[EUR][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	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv895108	chr10:45878908-46224333	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv895109	chr10:45882741-46210665	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv895112	chr10:46012620-46202216	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv895113	chr10:46134013-46167847	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3392795	chr10:46147995-46170942	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1045014	chr10:46148750-46814526	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	esv2754498	chr10:46148750-47136996	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv540591	chr10:46153700-47140487	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv1044906	chr10:46153700-47148281	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv540592	chr10:46153700-47148281	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv870020	chr10:46158215-47148490	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv1040524	chr10:46160537-47122043	Bivalent/Poised TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
14	nsv1038499	chr10:46160537-47140487	Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv540593	chr10:46160537-47140487	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv1055132	chr10:46160537-47148281	Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv540594	chr10:46160537-47148281	Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55893855	FAM21A///FAM21B	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46090600-46167600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:46108400-46167000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:46137200-46167000	Weak transcription	Right Ventricle	heart
4	chr10:46137600-46167200	Weak transcription	Ovary	ovary
5	chr10:46142800-46167000	Weak transcription	Esophagus	oesophagus
6	chr10:46142800-46167000	Weak transcription	Psoas Muscle	Psoas
7	chr10:46142800-46167000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr10:46142800-46167200	Weak transcription	Aorta	Aorta
9	chr10:46143200-46167000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr10:46143200-46167200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr10:46143200-46167400	Weak transcription	Left Ventricle	heart
12	chr10:46143400-46167000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr10:46143400-46167000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr10:46143600-46167200	Weak transcription	Fetal Lung	lung
15	chr10:46147200-46167000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr10:46149600-46167000	Weak transcription	Brain Hippocampus Middle	brain
17	chr10:46149600-46167200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr10:46149800-46163800	Weak transcription	Brain Anterior Caudate	brain
19	chr10:46152800-46167000	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr10:46154000-46167000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr10:46156800-46167000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr10:46156800-46167000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr10:46157000-46167000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr10:46157000-46167000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr10:46157000-46167000	Weak transcription	Fetal Intestine Small	intestine
26	chr10:46157000-46167000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr10:46157000-46167000	Weak transcription	Fetal Muscle Leg	muscle
28	chr10:46157000-46167000	Weak transcription	Lung	lung
29	chr10:46157200-46167000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr10:46157200-46167000	Weak transcription	Liver	Liver
31	chr10:46157400-46167200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr10:46157600-46166800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr10:46157800-46167000	Weak transcription	Thymus	Thymus
34	chr10:46158200-46165000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr10:46158200-46165200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr10:46158200-46167000	Weak transcription	Primary T cells from cord blood	blood
37	chr10:46158200-46167000	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr10:46158200-46167000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr10:46158200-46167000	Weak transcription	Dnd41	blood
40	chr10:46158200-46167400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr10:46158400-46167000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr10:46158400-46167200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr10:46158400-46167200	Weak transcription	Fetal Thymus	thymus
44	chr10:46158800-46167000	Weak transcription	Primary B cells from cord blood	blood
45	chr10:46159200-46167000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr10:46159400-46166800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr10:46162000-46162400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr10:46162200-46162400	Enhancers	GM12878-XiMat	blood

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