Variant report

Variant	rs4671024
Chromosome Location	chr2:33445658-33445659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:33294930..33295688-chr2:33444908..33445678,2	MCF-7	breast:
2	chr2:33440018..33441970-chr2:33445005..33447288,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10205739	0.82[CHB][hapmap]
rs10495784	0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1065324	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs11124310	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12611549	0.80[EUR][1000 genomes]
rs12617948	0.80[EUR][1000 genomes]
rs12617970	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs12620853	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs13021881	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1377946	0.81[ASN][1000 genomes]
rs1454376	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1454378	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1454379	0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17565877	0.82[CEU][hapmap]
rs17566780	0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs17567417	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17568051	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17641062	0.92[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs17641180	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17641906	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17642074	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1869542	0.81[CHB][hapmap]
rs1947444	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs2061026	0.81[EUR][1000 genomes]
rs2061027	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2290448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290449	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs2367508	0.82[AMR][1000 genomes]
rs2367623	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4474865	0.85[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap]
rs4630744	0.81[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4670245	0.80[EUR][1000 genomes]
rs4670307	0.81[CHB][hapmap]
rs4670313	0.88[ASN][1000 genomes]
rs4670778	0.89[CEU][hapmap];0.87[JPT][hapmap]
rs4670828	0.80[EUR][1000 genomes]
rs4670928	0.88[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs4671010	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4671016	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs4671035	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5006126	0.80[EUR][1000 genomes]
rs56163907	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58774073	0.85[ASN][1000 genomes]
rs58920936	0.83[ASN][1000 genomes]
rs60000782	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60558455	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62146726	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62146732	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62146734	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6543699	0.85[CEU][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs6705772	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6715793	0.82[JPT][hapmap]
rs6720405	0.80[EUR][1000 genomes]
rs6726760	0.84[ASN][1000 genomes]
rs726429	0.87[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs72797893	0.85[ASN][1000 genomes]
rs7580348	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7581446	0.82[EUR][1000 genomes]
rs7584473	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7590965	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7608222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608535	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964703	0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs996103	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	esv33628	chr2:33257484-33455355	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv873790	chr2:33369582-33466483	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4671024	LTBP1	cis	brain	BrainEAC

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33403800-33489800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:33414600-33455400	Weak transcription	Fetal Stomach	stomach
3	chr2:33436800-33455000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:33440400-33446000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:33440800-33447000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:33442200-33447000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:33442200-33447200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:33442600-33445800	Weak transcription	Right Ventricle	heart
9	chr2:33442600-33447600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:33442600-33452200	Weak transcription	Fetal Muscle Leg	muscle
11	chr2:33442600-33467600	Weak transcription	Ovary	ovary
12	chr2:33442800-33446200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:33442800-33446600	Weak transcription	Liver	Liver
14	chr2:33442800-33447200	Weak transcription	Left Ventricle	heart
15	chr2:33442800-33453400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:33442800-33471400	Weak transcription	Psoas Muscle	Psoas
17	chr2:33444200-33445800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr2:33444200-33445800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:33444200-33446000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr2:33444200-33446000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr2:33444400-33445800	Flanking Active TSS	A549	lung
22	chr2:33444400-33446000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr2:33444400-33446000	Enhancers	NH-A	brain
24	chr2:33444400-33446400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:33444400-33446600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr2:33444400-33446600	Enhancers	K562	blood
27	chr2:33444600-33445800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:33444600-33445800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr2:33444600-33446000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:33444600-33446000	Enhancers	Hela-S3	cervix
31	chr2:33444600-33446200	Enhancers	NHDF-Ad	bronchial
32	chr2:33444600-33446400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:33444600-33446400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:33444800-33446400	Enhancers	Placenta Amnion	Placenta Amnion
35	chr2:33444800-33446600	Enhancers	Fetal Heart	heart
36	chr2:33444800-33446600	Enhancers	Dnd41	blood
37	chr2:33444800-33446800	Enhancers	Fetal Lung	lung
38	chr2:33444800-33448400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:33444800-33448400	Enhancers	HMEC	breast
40	chr2:33445000-33445800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:33445000-33446000	Enhancers	H1 Cell Line	embryonic stem cell
42	chr2:33445000-33446000	Enhancers	Osteobl	bone
43	chr2:33445000-33446800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr2:33445200-33445800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:33445200-33446000	Enhancers	HUVEC	blood vessel
46	chr2:33445200-33446800	Enhancers	NHLF	lung
47	chr2:33445400-33445800	Weak transcription	Fetal Kidney	kidney
48	chr2:33445600-33445800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:33445600-33445800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:33445600-33446000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links