Variant report

Variant	rs16949275
Chromosome Location	chr18:44700703-44700704
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:44675372..44679287-chr18:44700113..44704114,10	MCF-7	breast:
2	chr18:44675406..44678402-chr18:44700257..44702641,2	K562	blood:
3	chr18:44676902..44678518-chr18:44699803..44701757,2	K562	blood:
4	chr18:44675848..44678361-chr18:44699497..44704011,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167220	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10083937	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10520715	0.90[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs11082563	0.87[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11082564	0.82[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11082566	0.83[ASN][1000 genomes]
rs11872531	0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11873315	0.83[ASN][1000 genomes]
rs11873812	0.83[ASN][1000 genomes]
rs11873880	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11874862	0.86[ASN][1000 genomes]
rs11875558	0.86[ASN][1000 genomes]
rs11875768	0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11877644	0.86[ASN][1000 genomes]
rs11877745	0.86[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];0.97[ASN][1000 genomes]
rs12326412	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];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12326457	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12326465	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12386076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12386092	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12386097	1.00[AFR][1000 genomes]
rs13547	0.82[CHB][hapmap]
rs1434528	0.82[CHB][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs16948914	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]
rs16948928	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]
rs16949157	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];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16950217	0.85[CEU][hapmap]
rs16952848	0.87[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs16958432	0.82[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs16958440	0.87[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs16958699	1.00[AFR][1000 genomes]
rs16958701	1.00[AFR][1000 genomes]
rs17711764	0.86[ASN][1000 genomes]
rs17712105	0.83[ASN][1000 genomes]
rs17712141	0.83[ASN][1000 genomes]
rs17712249	0.83[ASN][1000 genomes]
rs17784414	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17784795	0.90[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs17784867	0.83[ASN][1000 genomes]
rs2117373	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2289130	0.87[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2289131	0.85[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2289132	0.85[CEU][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes]
rs28578518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28587821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3809965	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3809966	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4609941	0.91[AFR][1000 genomes]
rs56395942	1.00[AFR][1000 genomes]
rs56654141	0.81[ASN][1000 genomes]
rs57744138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57928699	1.00[AFR][1000 genomes]
rs58061761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58715341	0.92[ASN][1000 genomes]
rs59217333	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60228288	1.00[AFR][1000 genomes]
rs60422392	1.00[AFR][1000 genomes]
rs60726022	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs60854219	1.00[AFR][1000 genomes]
rs61316646	1.00[AFR][1000 genomes]
rs61689863	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62095459	0.95[AFR][1000 genomes]
rs62096463	1.00[AFR][1000 genomes]
rs62096464	1.00[AFR][1000 genomes]
rs62096465	1.00[AFR][1000 genomes]
rs62096466	1.00[AFR][1000 genomes]
rs62096468	0.95[AFR][1000 genomes]
rs62096469	1.00[AFR][1000 genomes]
rs62096470	1.00[AFR][1000 genomes]
rs62096471	1.00[AFR][1000 genomes]
rs62096474	1.00[AFR][1000 genomes]
rs62096477	1.00[AFR][1000 genomes]
rs62096478	1.00[AFR][1000 genomes]
rs72907280	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs72909237	0.86[ASN][1000 genomes]
rs72909248	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv3412252	chr18:44684003-44711534	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16949275	HDHD2	cis	multi-tissue	Pritchard
rs16949275	HDHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44677800-44701000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr18:44677800-44701000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr18:44677800-44701000	Weak transcription	A549	lung
4	chr18:44677800-44701800	Weak transcription	Esophagus	oesophagus
5	chr18:44678000-44700800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr18:44678000-44701000	Weak transcription	Fetal Stomach	stomach
7	chr18:44678200-44700800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr18:44678200-44701000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr18:44678200-44701200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr18:44678200-44701200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr18:44678400-44700800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr18:44678400-44700800	Weak transcription	Lung	lung
13	chr18:44681800-44700800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr18:44681800-44700800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr18:44681800-44700800	Weak transcription	Placenta	Placenta
16	chr18:44681800-44701000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr18:44681800-44701000	Weak transcription	Fetal Thymus	thymus
18	chr18:44681800-44701200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr18:44682400-44701000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr18:44683000-44700800	Weak transcription	Fetal Intestine Large	intestine
21	chr18:44683000-44700800	Weak transcription	NH-A	brain
22	chr18:44683000-44701000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr18:44683000-44701200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr18:44685200-44700800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr18:44686800-44701200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr18:44687400-44701000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr18:44687600-44701000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr18:44688000-44701000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr18:44688200-44702200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr18:44689000-44701000	Weak transcription	Primary B cells from cord blood	blood
31	chr18:44690000-44701000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr18:44690200-44700800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr18:44690200-44701000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr18:44690200-44701000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr18:44690200-44701000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr18:44690600-44701000	Weak transcription	Osteobl	bone
37	chr18:44693600-44700800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr18:44693800-44701800	Weak transcription	Gastric	stomach
39	chr18:44695600-44701000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr18:44697200-44700800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr18:44698200-44701000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr18:44698600-44701200	Enhancers	K562	blood
43	chr18:44698600-44701600	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr18:44699000-44700800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr18:44699000-44700800	Weak transcription	HUVEC	blood vessel
46	chr18:44699000-44701000	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr18:44699000-44701000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr18:44699000-44701000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr18:44699000-44701000	Enhancers	Dnd41	blood
50	chr18:44699000-44701000	Enhancers	HepG2	liver

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