Variant report

Variant	rs1998840
Chromosome Location	chr10:95460373-95460374
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:95459724..95462239-chr10:95654343..95656368,2	K562	blood:
2	chr10:95439071..95442072-chr10:95459371..95461736,3	MCF-7	breast:
3	chr10:95275012..95277100-chr10:95460216..95463300,3	MCF-7	breast:
4	chr10:95459530..95461897-chr10:95501505..95503315,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138180	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10444062	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882299	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs10882302	0.86[ASN][1000 genomes]
rs10882303	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs10882319	0.93[ASN][1000 genomes]
rs11187580	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs11187582	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs11187583	0.86[ASN][1000 genomes]
rs11187584	0.86[ASN][1000 genomes]
rs11187585	0.86[ASN][1000 genomes]
rs11187596	1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11187599	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187616	0.87[ASN][1000 genomes]
rs11187620	1.00[ASN][1000 genomes]
rs11187644	0.85[ASN][1000 genomes]
rs45468996	0.86[ASN][1000 genomes]
rs7094280	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050705	chr10:95384527-95469255	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv540747	chr10:95384527-95469255	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv3346948	chr10:95421957-95532625	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv522686	chr10:95440286-95471338	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1998840	C10orf4	cis	thalamus	BrainEAC
rs1998840	FRA10AC1	cis	Artery Tibial	GTEx
rs1998840	C10orf4	Cis_1M	lymphoblastoid	RTeQTL
rs1998840	C10orf4	cis	brain	BrainEAC
rs1998840	FRA10AC1	cis	Muscle Skeletal	GTEx
rs1998840	FRA10AC1	cis	Nerve Tibial	GTEx
rs1998840	C10orf4	cis	intralobular white matter	BrainEAC

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:95417800-95461400	Weak transcription	Esophagus	oesophagus
2	chr10:95418400-95461400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr10:95418600-95460800	Weak transcription	Aorta	Aorta
4	chr10:95418600-95462000	Weak transcription	Spleen	Spleen
5	chr10:95425200-95461400	Weak transcription	K562	blood
6	chr10:95426000-95461400	Weak transcription	Colonic Mucosa	Colon
7	chr10:95429000-95460600	Weak transcription	Small Intestine	intestine
8	chr10:95430600-95461200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr10:95432400-95461200	Weak transcription	Stomach Mucosa	stomach
10	chr10:95438600-95461200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr10:95438600-95461400	Weak transcription	Gastric	stomach
12	chr10:95439200-95460600	Weak transcription	NHLF	lung
13	chr10:95439200-95461400	Weak transcription	Lung	lung
14	chr10:95439600-95461400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr10:95439800-95461000	Weak transcription	Fetal Heart	heart
16	chr10:95449200-95461400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr10:95449400-95461200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr10:95451800-95461400	Weak transcription	Right Ventricle	heart
19	chr10:95454200-95461400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr10:95454400-95461400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr10:95454400-95461400	Weak transcription	Pancreas	Pancrea
22	chr10:95454600-95461800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr10:95455800-95461000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr10:95456000-95460600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr10:95456000-95460800	Weak transcription	Hela-S3	cervix
26	chr10:95456000-95461000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr10:95456200-95460800	Weak transcription	NHEK	skin
28	chr10:95456200-95461000	Weak transcription	Brain Anterior Caudate	brain
29	chr10:95456200-95461200	Weak transcription	A549	lung
30	chr10:95456400-95460800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr10:95456800-95461000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr10:95457200-95461000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr10:95457200-95461400	Weak transcription	Thymus	Thymus
34	chr10:95457400-95460800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr10:95457400-95461000	Weak transcription	Fetal Kidney	kidney
36	chr10:95457400-95461000	Weak transcription	Fetal Lung	lung
37	chr10:95457400-95461200	Weak transcription	Brain Germinal Matrix	brain
38	chr10:95457400-95461200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr10:95457400-95461400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr10:95457600-95460800	Weak transcription	Colon Smooth Muscle	Colon
41	chr10:95457600-95461000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr10:95458200-95461200	Weak transcription	HSMMtube	muscle
43	chr10:95459000-95460400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr10:95459000-95460600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr10:95459000-95460600	Weak transcription	Fetal Intestine Small	intestine
46	chr10:95459000-95460600	Weak transcription	Psoas Muscle	Psoas
47	chr10:95459000-95461000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr10:95459000-95461000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr10:95459000-95461200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr10:95459200-95461400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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