Variant report

Variant	rs62365699
Chromosome Location	chr5:94050388-94050389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:94039956-94052296	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:94048115-94052802	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:94039895-94052973	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
MCTP1	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2973154	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs306572	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs430555	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72773602	0.91[EUR][1000 genomes]
rs7707464	0.86[ASN][1000 genomes]
rs845725	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462254	chr5:93956937-94056825	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv598953	chr5:93956937-94056825	ZNF genes & repeats Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv882387	chr5:94001476-94071404	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93995600-94050400	Weak transcription	Esophagus	oesophagus
2	chr5:94012600-94051000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr5:94012600-94053600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:94023200-94050400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr5:94023200-94051000	Weak transcription	Thymus	Thymus
6	chr5:94023400-94050400	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:94023400-94051800	Weak transcription	Fetal Intestine Small	intestine
8	chr5:94024600-94051800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:94025800-94050800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:94025800-94050800	Weak transcription	K562	blood
11	chr5:94025800-94051400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:94026400-94051600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr5:94028000-94050600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:94028000-94051600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:94029000-94051400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:94029200-94050400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr5:94029200-94051800	Weak transcription	Brain Germinal Matrix	brain
18	chr5:94029200-94052400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:94029400-94051200	Weak transcription	Fetal Brain Male	brain
20	chr5:94029400-94051400	Weak transcription	Fetal Heart	heart
21	chr5:94030200-94051400	Weak transcription	HSMM	muscle
22	chr5:94031000-94051200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr5:94031000-94052000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:94031200-94050600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:94034200-94051400	Weak transcription	Pancreas	Pancrea
26	chr5:94035400-94052000	Weak transcription	Fetal Kidney	kidney
27	chr5:94037400-94051000	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr5:94039000-94050800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr5:94039000-94064600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr5:94039800-94052000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr5:94040200-94050600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr5:94040800-94052400	Weak transcription	Fetal Stomach	stomach
33	chr5:94041400-94051400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr5:94041600-94050600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr5:94041800-94051600	Weak transcription	Brain Anterior Caudate	brain
36	chr5:94043200-94050600	Strong transcription	Hela-S3	cervix
37	chr5:94043200-94051000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:94043400-94050600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:94043600-94051000	Strong transcription	Fetal Thymus	thymus
40	chr5:94043600-94053000	Weak transcription	GM12878-XiMat	blood
41	chr5:94043800-94059400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr5:94044200-94051600	Weak transcription	HSMMtube	muscle
43	chr5:94044400-94052400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr5:94044600-94050600	Weak transcription	Fetal Lung	lung
45	chr5:94045400-94050400	Weak transcription	A549	lung
46	chr5:94045600-94050800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr5:94045600-94052000	Weak transcription	Right Ventricle	heart
48	chr5:94046800-94052200	Weak transcription	Spleen	Spleen
49	chr5:94047000-94051200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr5:94047200-94050400	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links