Variant report

Variant	rs55710849
Chromosome Location	chr19:40722927-40722928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40721117..40723953-chr19:40725760..40727528,2	K562	blood:
2	chr19:40714420..40716705-chr19:40721840..40724225,2	K562	blood:
3	chr19:40722781..40723282-chr20:35807520..35808173,2	MCF-7	breast:
4	chr19:40722262..40725312-chr19:40726429..40730380,4	MCF-7	breast:
5	chr19:40722002..40724261-chr19:40789079..40792675,3	MCF-7	breast:
6	chr19:40719578..40724896-chr19:40726262..40733162,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118705	Chromatin interaction
ENSG00000105219	Chromatin interaction
ENSG00000130758	Chromatin interaction
ENSG00000101353	Chromatin interaction
ENSG00000105221	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10423675	0.81[ASN][1000 genomes]
rs12460555	0.82[ASN][1000 genomes]
rs12609014	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304186	0.82[ASN][1000 genomes]
rs33933140	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34894858	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803317	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67322193	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs892117	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911698	chr19:40689580-40725304	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv911700	chr19:40695598-40725304	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv911701	chr19:40695598-40728417	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv911702	chr19:40697061-40731371	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv911703	chr19:40711333-40730279	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv911704	chr19:40716652-40730279	Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
11	nsv911705	chr19:40716652-40731371	ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
12	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55710849	MAP3K10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40711200-40731800	Weak transcription	Right Atrium	heart
2	chr19:40713200-40725200	Weak transcription	Hela-S3	cervix
3	chr19:40718600-40725200	Weak transcription	Dnd41	blood
4	chr19:40720600-40723200	Weak transcription	Brain Anterior Caudate	brain
5	chr19:40722000-40723000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:40722000-40723000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
7	chr19:40722000-40723400	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr19:40722000-40723400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
9	chr19:40722000-40723600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
10	chr19:40722000-40723800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr19:40722200-40723000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
12	chr19:40722200-40723000	Bivalent Enhancer	Colonic Mucosa	Colon
13	chr19:40722200-40723400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:40722200-40723400	Bivalent Enhancer	Fetal Brain Male	brain
15	chr19:40722200-40724200	Enhancers	Lung	lung
16	chr19:40722200-40724400	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr19:40722200-40724600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
18	chr19:40722400-40723200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:40722400-40723200	Bivalent Enhancer	Brain Hippocampus Middle	brain
20	chr19:40722400-40723200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
21	chr19:40722400-40723200	Bivalent Enhancer	Fetal Heart	heart
22	chr19:40722400-40723400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
23	chr19:40722400-40723800	Bivalent Enhancer	Placenta	Placenta
24	chr19:40722400-40724200	Enhancers	Pancreas	Pancrea
25	chr19:40722400-40724400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:40722600-40723000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
27	chr19:40722600-40723000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
28	chr19:40722600-40723000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
29	chr19:40722600-40723000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:40722600-40723000	Active TSS	Brain Cingulate Gyrus	brain
31	chr19:40722600-40723000	Enhancers	K562	blood
32	chr19:40722600-40723200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:40722600-40723400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:40722600-40723400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:40722600-40723600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:40722600-40723600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:40722600-40723800	Enhancers	Esophagus	oesophagus
38	chr19:40722600-40723800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
39	chr19:40722600-40724200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:40722800-40723000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
41	chr19:40722800-40723000	Bivalent Enhancer	Brain Germinal Matrix	brain
42	chr19:40722800-40723000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
43	chr19:40722800-40723000	Bivalent Enhancer	HSMMtube	muscle
44	chr19:40722800-40723200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
45	chr19:40722800-40723200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
46	chr19:40722800-40723200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr19:40722800-40723200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
48	chr19:40722800-40723200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr19:40722800-40723200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:40722800-40723200	Bivalent/Poised TSS	Fetal Intestine Small	intestine

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