Variant report

Variant	rs11876448
Chromosome Location	chr18:44644530-44644531
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10083937	0.82[CHB][hapmap]
rs10520715	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11082563	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11082564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11873315	0.82[AMR][1000 genomes]
rs11874862	0.82[AMR][1000 genomes]
rs11875558	0.82[AMR][1000 genomes]
rs11877644	0.82[AMR][1000 genomes]
rs11877745	0.82[AMR][1000 genomes]
rs12326412	0.82[CHB][hapmap]
rs12326465	0.81[CHB][hapmap]
rs12326600	0.80[ASN][1000 genomes]
rs12386076	0.96[ASN][1000 genomes]
rs12386092	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12386097	0.98[ASN][1000 genomes]
rs13547	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];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1434528	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16948914	1.00[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[ASN][1000 genomes]
rs16948928	1.00[ASW][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[ASN][1000 genomes]
rs16949275	0.82[CHB][hapmap]
rs16952848	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs16958432	1.00[ASW][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[ASN][1000 genomes]
rs16958440	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16958699	0.96[ASN][1000 genomes]
rs16958701	0.96[ASN][1000 genomes]
rs17711764	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17712105	0.82[AMR][1000 genomes]
rs17712141	0.82[AMR][1000 genomes]
rs17784414	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes]
rs17784795	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs17784867	0.82[AMR][1000 genomes]
rs2117373	1.00[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[ASN][1000 genomes]
rs2289130	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2289131	1.00[ASW][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];0.81[ASN][1000 genomes]
rs2289132	1.00[ASW][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs3809966	1.00[ASW][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap]
rs4609941	0.96[ASN][1000 genomes]
rs56395942	0.99[ASN][1000 genomes]
rs57468764	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57928699	0.96[ASN][1000 genomes]
rs58715341	0.86[AMR][1000 genomes]
rs60228288	0.93[ASN][1000 genomes]
rs60422392	0.94[ASN][1000 genomes]
rs60854219	0.96[ASN][1000 genomes]
rs61316646	0.84[ASN][1000 genomes]
rs61689863	0.96[ASN][1000 genomes]
rs62095459	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62096462	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62096463	0.94[ASN][1000 genomes]
rs62096464	0.94[ASN][1000 genomes]
rs62096465	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62096466	0.94[ASN][1000 genomes]
rs62096468	0.96[ASN][1000 genomes]
rs62096469	0.96[ASN][1000 genomes]
rs62096470	0.96[ASN][1000 genomes]
rs62096471	0.96[ASN][1000 genomes]
rs62096474	0.96[ASN][1000 genomes]
rs62096477	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62096478	0.96[ASN][1000 genomes]
rs72909237	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs72909248	0.82[AMR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11876448	HDHD2	Cis_1M	lymphoblastoid	RTeQTL
rs11876448	IER3IP1	cis	cerebellum	SCAN
rs11876448	HDHD2	cis	multi-tissue	Pritchard
rs11876448	HDHD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44620800-44675400	Weak transcription	A549	lung
2	chr18:44621600-44674400	Weak transcription	Small Intestine	intestine
3	chr18:44624200-44654200	Weak transcription	Fetal Heart	heart
4	chr18:44626600-44664800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr18:44629200-44675800	Weak transcription	HUVEC	blood vessel
6	chr18:44630200-44646400	Strong transcription	Primary B cells from cord blood	blood
7	chr18:44630600-44660400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr18:44632000-44654200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr18:44632400-44675800	Weak transcription	Stomach Mucosa	stomach
10	chr18:44636200-44670600	Weak transcription	Pancreas	Pancrea
11	chr18:44636600-44661000	Weak transcription	Psoas Muscle	Psoas
12	chr18:44637000-44647000	Weak transcription	Fetal Brain Male	brain
13	chr18:44638400-44660800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr18:44639200-44662400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr18:44639600-44660600	Weak transcription	NHLF	lung
16	chr18:44639600-44665000	Weak transcription	Colonic Mucosa	Colon
17	chr18:44639600-44666400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr18:44639800-44645000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr18:44639800-44654800	Weak transcription	HMEC	breast
20	chr18:44639800-44660600	Weak transcription	NH-A	brain
21	chr18:44639800-44660800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr18:44640000-44645000	Weak transcription	Fetal Kidney	kidney
23	chr18:44640400-44662000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr18:44640600-44646200	Weak transcription	GM12878-XiMat	blood
25	chr18:44640600-44675600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr18:44640800-44662000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr18:44641000-44653800	Weak transcription	HSMM	muscle
28	chr18:44641000-44654200	Weak transcription	Brain Anterior Caudate	brain
29	chr18:44641000-44654800	Weak transcription	Hela-S3	cervix
30	chr18:44641200-44644800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr18:44641200-44644800	Weak transcription	NHDF-Ad	bronchial
32	chr18:44641200-44645200	Weak transcription	HSMMtube	muscle
33	chr18:44641200-44654200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr18:44641200-44655600	Weak transcription	Fetal Brain Female	brain
35	chr18:44641200-44659600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr18:44641600-44644800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr18:44641600-44645200	Weak transcription	Brain Hippocampus Middle	brain
38	chr18:44641600-44645800	Weak transcription	Fetal Lung	lung
39	chr18:44641600-44654000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr18:44641600-44654200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr18:44641600-44654200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr18:44641600-44660400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr18:44641600-44670400	Weak transcription	HepG2	liver
44	chr18:44641600-44674000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr18:44641600-44675800	Weak transcription	Lung	lung
46	chr18:44641800-44644600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr18:44641800-44644800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr18:44641800-44644800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr18:44641800-44644800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr18:44641800-44644800	Weak transcription	Adipose Nuclei	Adipose

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