Variant report

Variant	rs2048431
Chromosome Location	chr1:155618630-155618631
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155247122..155248750-chr1:155618012..155619696,2	MCF-7	breast:
2	chr1:155615343..155618275-chr1:155618571..155621306,3	MCF-7	breast:
3	chr1:155617094..155622195-chr1:155655063..155661292,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143630	Chromatin interaction
ENSG00000163374	Chromatin interaction
ENSG00000132676	Chromatin interaction
ENSG00000176444	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10752611	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs10796945	0.88[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap]
rs10908469	0.92[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap]
rs10908470	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs10908471	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10908472	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10908479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908481	0.88[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs11264375	0.96[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs11264380	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs11264381	0.96[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs11264383	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11264386	0.92[EUR][1000 genomes]
rs11264387	0.96[CEU][hapmap];0.81[CHB][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs11264393	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11264397	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11264398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12022088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12030596	0.88[EUR][1000 genomes]
rs12035524	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12039893	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12040100	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12047626	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12047756	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079134	0.92[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap]
rs12093350	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12143948	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs12724079	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs12740629	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12744132	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12746592	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs12758945	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1360554	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs1556488	0.96[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs2175391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666826	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs28662267	0.81[EUR][1000 genomes]
rs34124416	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34620961	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34632540	0.83[ASN][1000 genomes]
rs348186	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348196	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35615695	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs3738590	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3851912	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3892792	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs4550031	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs475550	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971095	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427278	0.91[EUR][1000 genomes]
rs6427286	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs644853	0.91[JPT][hapmap]
rs6672128	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6688636	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs6696888	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs670876	0.84[CEU][hapmap];0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs678157	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs708611	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs7411786	0.84[EUR][1000 genomes]
rs7521594	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7541060	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs821551	0.91[JPT][hapmap]
rs860295	0.85[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	esv3431739	chr1:155514331-155664183	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	esv3388968	chr1:155532335-155658278	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv1002390	chr1:155553423-155706930	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv436522	chr1:155559513-155674249	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv946419	chr1:155561148-155630744	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	esv3360339	chr1:155562157-155683127	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
10	nsv547965	chr1:155563152-155688600	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
11	esv3381327	chr1:155582853-155718436	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
12	esv3436971	chr1:155618172-155733386	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
13	esv3338099	chr1:155618190-155733359	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2048431	SPRR2A	cis	cerebellum	SCAN
rs2048431	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs2048431	FDPS	cis	parietal	SCAN
rs2048431	RIT1	cis	cerebellum	SCAN
rs2048431	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs2048431	YY1AP1	cis	cerebellum	SCAN
rs2048431	GBA	cis	Esophagus Mucosa	GTEx
rs2048431	YY1AP1	cis	parietal	SCAN
rs2048431	GPATCH4	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155607400-155621200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:155614000-155621000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:155614800-155618800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:155615200-155621600	Weak transcription	Aorta	Aorta
5	chr1:155615400-155628600	Weak transcription	Right Ventricle	heart
6	chr1:155615600-155628400	Weak transcription	Left Ventricle	heart
7	chr1:155615600-155628400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:155615800-155620400	Weak transcription	Lung	lung
9	chr1:155616000-155628200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:155616200-155620800	Weak transcription	Fetal Brain Male	brain
11	chr1:155616400-155628800	Weak transcription	Small Intestine	intestine
12	chr1:155617000-155628400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:155617200-155620000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr1:155617400-155622000	Enhancers	Placenta	Placenta
15	chr1:155617800-155637000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:155618000-155618800	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr1:155618000-155618800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:155618000-155618800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:155618000-155618800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:155618000-155618800	Enhancers	Brain Hippocampus Middle	brain
21	chr1:155618000-155618800	Enhancers	Colon Smooth Muscle	Colon
22	chr1:155618000-155618800	Enhancers	Fetal Stomach	stomach
23	chr1:155618000-155618800	Flanking Active TSS	A549	lung
24	chr1:155618000-155618800	Flanking Active TSS	Hela-S3	cervix
25	chr1:155618000-155618800	Enhancers	HepG2	liver
26	chr1:155618000-155618800	Enhancers	HUVEC	blood vessel
27	chr1:155618000-155618800	Enhancers	K562	blood
28	chr1:155618000-155618800	Flanking Active TSS	NH-A	brain
29	chr1:155618000-155618800	Flanking Active TSS	NHEK	skin
30	chr1:155618000-155619000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:155618000-155619000	Enhancers	Fetal Intestine Small	intestine
32	chr1:155618000-155619000	Enhancers	Stomach Mucosa	stomach
33	chr1:155618000-155619000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr1:155618200-155618800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:155618200-155618800	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr1:155618200-155618800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:155618200-155618800	Enhancers	Colonic Mucosa	Colon
38	chr1:155618200-155618800	Enhancers	Duodenum Mucosa	Duodenum
39	chr1:155618200-155618800	Enhancers	Fetal Lung	lung
40	chr1:155618200-155618800	Enhancers	Rectal Smooth Muscle	rectum
41	chr1:155618200-155619000	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr1:155618200-155619000	Enhancers	Liver	Liver
43	chr1:155618200-155619000	Enhancers	Brain Angular Gyrus	brain
44	chr1:155618200-155619000	Enhancers	Brain Substantia Nigra	brain
45	chr1:155618400-155618800	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr1:155618400-155618800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:155618400-155618800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:155618400-155618800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:155618400-155618800	Enhancers	Adipose Nuclei	Adipose
50	chr1:155618400-155618800	Enhancers	NHDF-Ad	bronchial

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