Variant report

Variant	rs17854567
Chromosome Location	chr10:46143958-46143959
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MARCH8-3	chr10:46143742-46143982	NR_104256

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12257537	0.86[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs1906284	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2305299	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59390133	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72798228	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430166	chr10:45668894-46148794	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv1050880	chr10:46091441-46160597	Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv540588	chr10:46091441-46160597	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	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
9	nsv540589	chr10:46136345-46153760	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17854567	FAM21C	cis	multi-tissue	Pritchard
rs17854567	FAM21A///FAM21B	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46090600-46167600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:46098200-46153400	Weak transcription	HSMM	muscle
3	chr10:46104400-46151400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr10:46106800-46146400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr10:46108000-46155800	Weak transcription	Brain Angular Gyrus	brain
6	chr10:46108400-46149400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr10:46108400-46167000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:46108600-46149200	Weak transcription	Brain Hippocampus Middle	brain
9	chr10:46108600-46155400	Weak transcription	Fetal Intestine Small	intestine
10	chr10:46110200-46153800	Weak transcription	NH-A	brain
11	chr10:46110800-46156800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr10:46112200-46152400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr10:46119800-46148200	Weak transcription	Colonic Mucosa	Colon
14	chr10:46120000-46157800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr10:46120200-46148400	Weak transcription	Small Intestine	intestine
16	chr10:46122200-46154600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr10:46122200-46157200	Weak transcription	Gastric	stomach
18	chr10:46122400-46149000	Weak transcription	Brain Substantia Nigra	brain
19	chr10:46122400-46156400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:46130800-46147600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:46133800-46157800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr10:46134800-46147600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr10:46135800-46144200	Weak transcription	Brain Germinal Matrix	brain
24	chr10:46137200-46167000	Weak transcription	Right Ventricle	heart
25	chr10:46137600-46149000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr10:46137600-46156600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr10:46137600-46167200	Weak transcription	Ovary	ovary
28	chr10:46138000-46148200	Weak transcription	Fetal Brain Female	brain
29	chr10:46138400-46144200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr10:46138400-46156600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr10:46138600-46147400	Strong transcription	Primary T cells from cord blood	blood
32	chr10:46138600-46148000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr10:46139400-46144200	Strong transcription	Primary hematopoietic stem cells	blood
34	chr10:46139400-46148000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr10:46139600-46144200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr10:46139800-46144200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr10:46140000-46144400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr10:46140000-46144400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr10:46140400-46144000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr10:46140600-46144000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr10:46140600-46144200	Strong transcription	Dnd41	blood
42	chr10:46140600-46144400	Strong transcription	Fetal Thymus	thymus
43	chr10:46140600-46150200	Weak transcription	HepG2	liver
44	chr10:46141200-46144400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr10:46141200-46147200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr10:46141400-46144000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr10:46141400-46144000	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr10:46141400-46144200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr10:46141400-46144200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr10:46141400-46144200	Strong transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links