Variant report

Variant	rs16948928
Chromosome Location	chr18:44675821-44675822
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:44673432..44675834-chr18:44691617..44693277,2	MCF-7	breast:
2	chr18:44675372..44679287-chr18:44700113..44704114,10	MCF-7	breast:
3	chr18:44660900..44663835-chr18:44675479..44677959,3	MCF-7	breast:
4	chr18:44663118..44666144-chr18:44673724..44676472,4	K562	blood:

Variant related genes	Relation type
ENSG00000267228	Chromatin interaction
ENSG00000267800	Chromatin interaction
ENSG00000134049	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10083937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10520715	0.81[CHB][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap]
rs11082563	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11082564	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11872531	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11873880	1.00[AFR][1000 genomes]
rs11875768	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11876448	0.96[ASN][1000 genomes]
rs12326122	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12326221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12326412	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12326457	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12326465	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12326600	0.83[ASN][1000 genomes]
rs12386076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12386092	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];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12386097	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13547	1.00[ASW][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[ASN][1000 genomes]
rs1434528	1.00[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs16948914	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16949157	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16949275	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16950217	0.85[CEU][hapmap]
rs16952848	0.85[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16958432	1.00[ASW][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16958440	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16958699	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16958701	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17784414	0.80[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs17784795	0.81[CHB][hapmap];1.00[GIH][hapmap]
rs2117373	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289130	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2289131	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2289132	1.00[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs28578518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28587821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3809965	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3809966	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4609941	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56395942	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs57468764	0.95[ASN][1000 genomes]
rs57744138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57928699	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58061761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59217333	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60228288	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs60422392	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs60726022	0.91[AFR][1000 genomes]
rs60854219	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61316646	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs61689863	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62095459	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62096462	0.95[ASN][1000 genomes]
rs62096463	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62096464	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62096465	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62096466	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62096468	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62096469	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62096470	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62096471	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62096474	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62096477	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62096478	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72907280	1.00[AFR][1000 genomes]
rs998818	1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv833640	chr18:44552276-44714872	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv909612	chr18:44560875-44681485	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv576819	chr18:44602249-44677627	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv909613	chr18:44644530-44690107	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16948928	HDHD2	cis	multi-tissue	Pritchard
rs16948928	HDHD2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44663400-44676000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr18:44673000-44676000	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr18:44674000-44676000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr18:44674400-44676200	Enhancers	Small Intestine	intestine
5	chr18:44674800-44676000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr18:44675000-44676000	Weak transcription	Aorta	Aorta
7	chr18:44675000-44678000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr18:44675200-44676000	Enhancers	Thymus	Thymus
9	chr18:44675200-44676200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr18:44675200-44677200	Active TSS	K562	blood
11	chr18:44675400-44676000	Enhancers	Primary T cells from cord blood	blood
12	chr18:44675400-44676000	Enhancers	Primary hematopoietic stem cells	blood
13	chr18:44675400-44676000	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr18:44675400-44676000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr18:44675400-44676200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr18:44675400-44676400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr18:44675400-44676400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr18:44675400-44676400	Flanking Active TSS	Dnd41	blood
19	chr18:44675400-44677400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr18:44675400-44677400	Active TSS	A549	lung
21	chr18:44675400-44677600	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr18:44675400-44677600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr18:44675400-44678200	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr18:44675600-44676000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr18:44675600-44676000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr18:44675600-44676000	Enhancers	Primary B cells from peripheral blood	blood
27	chr18:44675600-44676000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr18:44675600-44676000	Flanking Active TSS	Fetal Intestine Small	intestine
29	chr18:44675600-44676000	Flanking Active TSS	Fetal Stomach	stomach
30	chr18:44675600-44676000	Enhancers	Placenta Amnion	Placenta Amnion
31	chr18:44675600-44676200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr18:44675600-44676200	Flanking Active TSS	Brain Germinal Matrix	brain
33	chr18:44675600-44676200	Flanking Active TSS	GM12878-XiMat	blood
34	chr18:44675600-44676200	Flanking Active TSS	HMEC	breast
35	chr18:44675600-44676200	Flanking Active TSS	HSMMtube	muscle
36	chr18:44675600-44676200	Flanking Active TSS	NHEK	skin
37	chr18:44675600-44676200	Flanking Active TSS	Osteobl	bone
38	chr18:44675600-44676400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr18:44675600-44676400	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr18:44675600-44676400	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr18:44675600-44676400	Flanking Active TSS	Hela-S3	cervix
42	chr18:44675600-44676600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr18:44675600-44676600	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr18:44675600-44677200	Active TSS	NHLF	lung
45	chr18:44675600-44677400	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr18:44675600-44677400	Active TSS	NHDF-Ad	bronchial
47	chr18:44675600-44677600	Active TSS	H1 Cell Line	embryonic stem cell
48	chr18:44675600-44677600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr18:44675600-44677600	Active TSS	Brain Angular Gyrus	brain
50	chr18:44675600-44677600	Active TSS	Duodenum Smooth Muscle	Duodenum

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