Variant report

Variant	rs4975180
Chromosome Location	chr4:129198402-129198403
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	chr4:129198119-129198416	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:129195768..129200142-chr4:129201201..129205010,4	K562	blood:
2	chr4:129197174..129201626-chr4:129202909..129211049,8	MCF-7	breast:
3	chr4:129197371..129203827-chr4:129206171..129210095,7	MCF-7	breast:
4	chr4:129197097..129200705-chr4:129202397..129205542,4	MCF-7	breast:

Variant related genes	Relation type
PGRMC2	TF binding region
ENSG00000164040	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11098953	0.87[ASN][1000 genomes]
rs11098954	0.83[CEU][hapmap];0.87[ASN][1000 genomes]
rs11728141	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11733374	0.96[EUR][1000 genomes]
rs12650034	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13103317	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13103695	0.96[EUR][1000 genomes]
rs1391980	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1403125	0.96[EUR][1000 genomes]
rs1522432	0.96[EUR][1000 genomes]
rs1829726	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1851399	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1851400	0.96[EUR][1000 genomes]
rs2036687	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2101808	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2202805	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2391257	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28609279	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs290004	0.83[ASN][1000 genomes]
rs34174952	0.96[EUR][1000 genomes]
rs34837036	0.83[ASN][1000 genomes]
rs3755896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs430431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4624668	0.95[EUR][1000 genomes]
rs4975220	1.00[CEU][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes]
rs4975299	0.87[ASN][1000 genomes]
rs62318161	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6814132	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6816625	0.88[ASN][1000 genomes]
rs6842987	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6849992	0.88[ASN][1000 genomes]
rs7666566	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7679633	0.96[EUR][1000 genomes]
rs7691103	0.95[EUR][1000 genomes]
rs9790593	0.87[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390887	chr4:128932563-129207255	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4975180	LARP2	cis	multi-tissue	Pritchard
rs4975180	HSPA4L	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129173800-129207400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:129184600-129206200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:129187800-129206400	Weak transcription	Ovary	ovary
4	chr4:129187800-129206600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:129187800-129207200	Weak transcription	Aorta	Aorta
6	chr4:129188600-129205800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr4:129188800-129203600	Weak transcription	Stomach Mucosa	stomach
8	chr4:129188800-129206200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:129189000-129200800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:129189000-129205600	Weak transcription	Fetal Lung	lung
11	chr4:129189400-129198800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:129189400-129206000	Weak transcription	Fetal Stomach	stomach
13	chr4:129189400-129207200	Weak transcription	Thymus	Thymus
14	chr4:129189600-129200800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:129189800-129205400	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:129190000-129206000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:129190200-129200400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr4:129190400-129201000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:129190600-129205400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:129190600-129206200	Weak transcription	Psoas Muscle	Psoas
21	chr4:129190600-129206600	Weak transcription	Brain Anterior Caudate	brain
22	chr4:129191000-129206200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:129191400-129207800	Weak transcription	Esophagus	oesophagus
24	chr4:129191600-129200600	Weak transcription	Fetal Brain Female	brain
25	chr4:129191600-129206600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr4:129191600-129207400	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:129191800-129205400	Weak transcription	Fetal Brain Male	brain
28	chr4:129192400-129200600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr4:129192400-129205800	Weak transcription	Fetal Kidney	kidney
30	chr4:129192400-129206200	Weak transcription	Brain Germinal Matrix	brain
31	chr4:129192600-129207800	Weak transcription	Lung	lung
32	chr4:129192800-129206200	Weak transcription	Primary B cells from cord blood	blood
33	chr4:129192800-129207200	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr4:129193000-129199200	Weak transcription	Right Ventricle	heart
35	chr4:129193000-129201800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:129193000-129203800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:129193000-129204400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:129193000-129205400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr4:129193000-129206400	Weak transcription	Left Ventricle	heart
40	chr4:129193000-129207400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr4:129193200-129200800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr4:129193200-129202200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr4:129193400-129203200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:129193400-129203200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr4:129193400-129204400	Weak transcription	Fetal Intestine Large	intestine
46	chr4:129193400-129204600	Weak transcription	Fetal Muscle Leg	muscle
47	chr4:129193400-129205200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr4:129193400-129205400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr4:129193400-129205400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:129193400-129206000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links