Variant report

Variant	rs4846219
Chromosome Location	chr1:10463888-10463889
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10457481..10460919-chr1:10461476..10464361,6	MCF-7	breast:
2	chr1:10448039..10452372-chr1:10461454..10464650,4	MCF-7	breast:
3	chr1:10457799..10462480-chr1:10462835..10469512,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265945	Chromatin interaction
ENSG00000142657	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs1002076	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10492969	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap]
rs10492971	1.00[JPT][hapmap]
rs10492972	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10492973	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs10864450	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs10864453	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs11121541	0.87[EUR][1000 genomes]
rs11121543	0.94[YRI][hapmap]
rs11121551	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11121552	0.83[CHD][hapmap]
rs11121555	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11121557	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11121560	0.93[ASN][1000 genomes]
rs11121561	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11121563	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11121566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1138791	0.91[ASN][1000 genomes]
rs11576384	0.94[ASN][1000 genomes]
rs11579365	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11582123	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11585794	0.84[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs11586842	0.88[ASN][1000 genomes]
rs11587309	0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11587495	0.83[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs11587854	0.91[ASN][1000 genomes]
rs12064209	0.94[YRI][hapmap]
rs12069853	0.94[YRI][hapmap]
rs12118323	0.96[ASN][1000 genomes]
rs12120042	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12120191	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12127604	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12128374	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12130220	0.83[CHD][hapmap]
rs12130563	0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12131441	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12133617	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12136376	0.83[CHD][hapmap]
rs12136404	0.80[EUR][1000 genomes]
rs12141201	0.91[ASN][1000 genomes]
rs12141246	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs12141416	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12402723	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12403443	0.83[CHD][hapmap]
rs12407992	0.83[CHD][hapmap]
rs12409754	0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12734551	0.83[CHD][hapmap]
rs12737239	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs12746471	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12757288	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1339458	0.83[CHD][hapmap]
rs1467653	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs1536262	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1538557	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1555849	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1556916	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1556917	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17034643	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17034821	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17396973	0.80[EUR][1000 genomes]
rs17400510	0.83[CHD][hapmap]
rs17401924	0.83[CHD][hapmap]
rs17401966	0.83[CHD][hapmap]
rs17402762	0.90[EUR][1000 genomes]
rs17410217	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17411502	0.83[CHD][hapmap]
rs1889309	0.83[CHD][hapmap]
rs2027330	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2039778	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2148152	0.80[ASN][1000 genomes]
rs2182326	0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap]
rs2185252	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2229687	0.96[ASN][1000 genomes]
rs2236678	0.96[ASN][1000 genomes]
rs2275424	0.81[CHD][hapmap]
rs34045426	0.93[ASN][1000 genomes]
rs34075302	0.89[ASN][1000 genomes]
rs35716098	0.96[ASN][1000 genomes]
rs35759975	0.96[ASN][1000 genomes]
rs35811280	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3737155	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3748575	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs3748577	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3748578	0.83[CHD][hapmap]
rs3748581	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3753037	0.83[CHD][hapmap]
rs3762286	0.96[ASN][1000 genomes]
rs3762287	0.93[ASN][1000 genomes]
rs3762288	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240911	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4333852	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4348727	0.81[CHD][hapmap]
rs4475756	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4529713	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4623	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs4845930	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4846197	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4846198	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs4846199	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs4846207	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs4846208	0.83[CHD][hapmap]
rs4846209	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4846210	0.83[CHD][hapmap]
rs4846212	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4846216	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4846218	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4846221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58014725	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61778399	0.80[ASN][1000 genomes]
rs61778401	0.80[ASN][1000 genomes]
rs61778402	0.80[ASN][1000 genomes]
rs61778404	0.87[ASN][1000 genomes]
rs6541085	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs6541089	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs6541090	0.88[EUR][1000 genomes]
rs6541094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674843	0.83[CHD][hapmap]
rs6674949	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6682868	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6696056	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs6703708	0.94[YRI][hapmap]
rs746881	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7520935	0.83[CHD][hapmap]
rs7546364	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7546368	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs7553228	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7553935	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs8019	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs912962	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs912963	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9332414	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs946501	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs946503	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs946504	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs9651117	0.93[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	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats 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	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4846219	PGD	cis	parietal	SCAN
rs4846219	PGD	cis	lymphoblastoid	seeQTL
rs4846219	PLEKHG5	cis	parietal	SCAN
rs4846219	PGD	Cis_1M	lymphoblastoid	RTeQTL
rs4846219	PGD	cis	multi-tissue	Pritchard
rs4846219	APITD1	cis	cerebellum	SCAN
rs4846219	MTOR	cis	parietal	SCAN
rs4846219	PGD	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10459600-10465000	Transcr. at gene 5' and 3'	A549	lung
2	chr1:10460000-10490200	Weak transcription	Psoas Muscle	Psoas
3	chr1:10460200-10475400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:10460400-10464200	Weak transcription	Pancreas	Pancrea
5	chr1:10460400-10464200	Weak transcription	Spleen	Spleen
6	chr1:10460400-10464800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:10460400-10472800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:10460400-10475200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:10460600-10464000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:10460600-10464200	Weak transcription	Small Intestine	intestine
11	chr1:10460600-10481200	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr1:10460800-10464200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:10460800-10468800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:10460800-10480400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:10460800-10482000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:10460800-10482400	Strong transcription	Fetal Stomach	stomach
17	chr1:10460800-10483400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:10461000-10464200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:10461000-10464600	Genic enhancers	HUVEC	blood vessel
20	chr1:10461000-10474600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:10461000-10475200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:10461000-10476800	Weak transcription	Fetal Heart	heart
23	chr1:10461000-10482000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:10461200-10464200	Genic enhancers	Hela-S3	cervix
25	chr1:10461200-10464400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:10461200-10464400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:10461200-10482000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:10461200-10482000	Strong transcription	Fetal Muscle Leg	muscle
29	chr1:10461200-10490000	Weak transcription	Right Atrium	heart
30	chr1:10461400-10464400	Genic enhancers	NH-A	brain
31	chr1:10461400-10475200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:10461400-10483000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:10461400-10483000	Strong transcription	Fetal Intestine Small	intestine
34	chr1:10461400-10483400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr1:10461600-10465200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:10461600-10481800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:10461600-10482800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:10461800-10465000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
39	chr1:10461800-10472800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr1:10461800-10473600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:10461800-10473600	Strong transcription	Primary hematopoietic stem cells	blood
42	chr1:10461800-10473600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:10461800-10473600	Strong transcription	Rectal Smooth Muscle	rectum
44	chr1:10461800-10474200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:10461800-10475200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:10461800-10482000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:10461800-10482000	Strong transcription	Dnd41	blood
48	chr1:10462000-10473000	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr1:10462000-10475200	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr1:10462000-10482000	Strong transcription	Fetal Intestine Large	intestine

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