Variant report

Variant	rs1001848
Chromosome Location	chr1:155047379-155047380
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155045594..155047619-chr1:155101615..155103329,2	K562	blood:
2	chr1:155013927..155032770-chr1:155044175..155061131,53	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232093	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000169242	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10157801	0.85[JPT][hapmap]
rs10908454	1.00[JPT][hapmap]
rs10908455	1.00[JPT][hapmap]
rs10908456	1.00[JPT][hapmap]
rs10908458	0.85[JPT][hapmap]
rs11264304	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs11264306	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264311	0.82[AFR][1000 genomes]
rs11264314	1.00[JPT][hapmap]
rs11264319	1.00[JPT][hapmap]
rs11264329	1.00[JPT][hapmap]
rs12025371	0.85[JPT][hapmap]
rs12028043	0.85[JPT][hapmap]
rs12040970	1.00[JPT][hapmap]
rs12047986	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145362	1.00[JPT][hapmap]
rs12904	0.85[JPT][hapmap]
rs1462855	1.00[JPT][hapmap]
rs1564124	0.86[ASN][1000 genomes]
rs1870939	1.00[JPT][hapmap]
rs2306124	1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[AFR][1000 genomes]
rs35902694	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs3765087	1.00[JPT][hapmap]
rs3766916	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3806256	0.85[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4045192	0.85[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs4246529	0.85[JPT][hapmap]
rs4276913	0.85[JPT][hapmap]
rs4745	0.85[JPT][hapmap]
rs4845407	1.00[JPT][hapmap]
rs4845408	1.00[JPT][hapmap]
rs4845712	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4971052	1.00[JPT][hapmap]
rs4971066	0.85[JPT][hapmap]
rs4971073	0.85[JPT][hapmap]
rs4971076	0.85[JPT][hapmap]
rs4971079	0.85[JPT][hapmap]
rs6427158	1.00[JPT][hapmap]
rs6665822	1.00[JPT][hapmap]
rs6693477	1.00[JPT][hapmap]
rs7364524	0.85[JPT][hapmap]
rs7365544	1.00[JPT][hapmap]
rs7367207	1.00[JPT][hapmap]
rs7367897	1.00[JPT][hapmap]
rs7368345	1.00[JPT][hapmap]
rs7534162	1.00[JPT][hapmap]
rs7548955	1.00[JPT][hapmap]
rs9297	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
3	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
4	nsv872455	chr1:155003954-155106550	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1001848	APOA1BP	cis	cerebellum	SCAN
rs1001848	UBE2Q1	cis	cerebellum	SCAN
rs1001848	SMCP	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155043800-155050800	Weak transcription	A549	lung
2	chr1:155044000-155048000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:155044000-155051000	Weak transcription	Pancreas	Pancrea
4	chr1:155044000-155051000	Weak transcription	Right Atrium	heart
5	chr1:155044200-155047400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr1:155044200-155050000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:155044200-155050800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:155044600-155050600	Weak transcription	Spleen	Spleen
9	chr1:155044600-155050800	Weak transcription	Lung	lung
10	chr1:155044600-155051000	Weak transcription	Gastric	stomach
11	chr1:155044800-155050400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:155045800-155047800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:155046000-155047800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:155046000-155048200	Weak transcription	K562	blood
15	chr1:155046200-155047400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr1:155046200-155048200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:155046400-155049600	Weak transcription	Fetal Intestine Small	intestine
18	chr1:155046400-155050000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:155046400-155050600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr1:155046400-155051000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:155046400-155051000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:155046600-155049800	Weak transcription	HMEC	breast
23	chr1:155046600-155050000	Weak transcription	Esophagus	oesophagus
24	chr1:155046600-155050000	Weak transcription	NHEK	skin
25	chr1:155046600-155050400	Enhancers	Primary T cells from cord blood	blood
26	chr1:155046600-155050600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:155046600-155050600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:155046600-155050800	Weak transcription	GM12878-XiMat	blood
29	chr1:155046600-155051000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:155046600-155051200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:155046800-155050600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:155046800-155050800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:155046800-155051000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:155047200-155048200	Bivalent Enhancer	Fetal Thymus	thymus
35	chr1:155047200-155048800	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr1:155047200-155050800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:155047200-155051000	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links