Variant report

Variant	rs1055592
Chromosome Location	chr14:77743644-77743645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:77741494..77746628-chr14:77751488..77756217,6	MCF-7	breast:
2	chr14:77742580..77744356-chr14:77768244..77771004,2	MCF-7	breast:
3	chr14:77741661..77744211-chr14:77747237..77749936,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000009830	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10138030	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs11547793	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11624564	0.89[CHD][hapmap]
rs2270422	0.82[CHB][hapmap]
rs2287387	0.86[CHD][hapmap]
rs2287388	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs2287392	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs368855	0.91[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3783986	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs3783988	0.92[ASW][hapmap];0.94[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3783989	0.94[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs449345	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4903567	0.86[CHD][hapmap]
rs61990291	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6636	0.82[CHB][hapmap]
rs7158951	0.89[CHD][hapmap]
rs7159558	0.86[CHD][hapmap]
rs8009261	0.89[CHD][hapmap]
rs8009733	0.89[CHD][hapmap]
rs878908	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][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	nsv431017	chr14:76938089-77854647	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv1361	chr14:77707417-77753024	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv902104	chr14:77720741-77756321	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1055592	POMT2	cis	parietal	SCAN
rs1055592	EIF2B2	cis	cerebellum	SCAN
rs1055592	ESRRB	cis	parietal	SCAN
rs1055592	ENTPD5	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77738800-77749600	Weak transcription	NHDF-Ad	bronchial
2	chr14:77739000-77749800	Weak transcription	HUVEC	blood vessel
3	chr14:77739400-77744600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr14:77739400-77745400	Weak transcription	Fetal Lung	lung
5	chr14:77739400-77749000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr14:77739600-77744400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr14:77739600-77745400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr14:77739600-77745600	Weak transcription	Primary B cells from cord blood	blood
9	chr14:77739600-77775600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr14:77739800-77743800	Weak transcription	HSMMtube	muscle
11	chr14:77740000-77744600	Weak transcription	Colonic Mucosa	Colon
12	chr14:77740000-77744600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr14:77740000-77749600	Weak transcription	HMEC	breast
14	chr14:77740200-77746400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr14:77740200-77749600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr14:77740200-77750800	Weak transcription	Fetal Thymus	thymus
17	chr14:77740200-77766800	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr14:77740200-77769800	Weak transcription	Small Intestine	intestine
19	chr14:77740400-77746200	Weak transcription	NHEK	skin
20	chr14:77740400-77749200	Weak transcription	Osteobl	bone
21	chr14:77740400-77766000	Weak transcription	Stomach Mucosa	stomach
22	chr14:77740600-77744400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr14:77740600-77744400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr14:77740800-77758000	Strong transcription	Fetal Stomach	stomach
25	chr14:77740800-77766200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr14:77741000-77749600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr14:77741000-77750000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr14:77741000-77750400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr14:77741000-77767400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr14:77741200-77745200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr14:77741200-77749400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr14:77741400-77753600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr14:77741600-77744400	Weak transcription	HepG2	liver
34	chr14:77741800-77746600	Strong transcription	Brain Germinal Matrix	brain
35	chr14:77741800-77749000	Strong transcription	Fetal Intestine Small	intestine
36	chr14:77741800-77749400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr14:77741800-77752000	Weak transcription	Psoas Muscle	Psoas
38	chr14:77741800-77755400	Strong transcription	Fetal Muscle Leg	muscle
39	chr14:77741800-77757200	Strong transcription	Liver	Liver
40	chr14:77741800-77758600	Strong transcription	Fetal Muscle Trunk	muscle
41	chr14:77741800-77773600	Weak transcription	GM12878-XiMat	blood
42	chr14:77742000-77744400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr14:77742000-77744400	Strong transcription	Esophagus	oesophagus
44	chr14:77742000-77744600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr14:77742000-77747800	Weak transcription	HSMM	muscle
46	chr14:77742000-77749200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr14:77742000-77749400	Weak transcription	NH-A	brain
48	chr14:77742000-77756800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr14:77742000-77757400	Weak transcription	Right Atrium	heart
50	chr14:77742000-77766600	Strong transcription	Placenta	Placenta

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