Variant report

Variant	rs4609941
Chromosome Location	chr18:44645491-44645492
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10083937	0.91[AFR][1000 genomes]
rs11082563	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11082564	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11872531	0.91[AFR][1000 genomes]
rs11873880	0.91[AFR][1000 genomes]
rs11875768	0.91[AFR][1000 genomes]
rs11876448	0.96[ASN][1000 genomes]
rs12326122	0.83[AFR][1000 genomes]
rs12326221	0.91[AFR][1000 genomes]
rs12326412	0.91[AFR][1000 genomes]
rs12326457	0.91[AFR][1000 genomes]
rs12326600	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12386076	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12386092	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12386097	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13547	0.95[ASN][1000 genomes]
rs1434528	0.95[ASN][1000 genomes]
rs16948914	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16948928	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16949157	0.91[AFR][1000 genomes]
rs16949275	0.91[AFR][1000 genomes]
rs16952848	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16958432	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16958440	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16958699	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958701	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17784414	0.87[AFR][1000 genomes]
rs2117373	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2289130	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289131	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2289132	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28578518	0.91[AFR][1000 genomes]
rs28587821	0.91[AFR][1000 genomes]
rs3809965	0.91[AFR][1000 genomes]
rs3809966	0.91[AFR][1000 genomes]
rs56395942	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs57468764	0.95[ASN][1000 genomes]
rs57744138	0.91[AFR][1000 genomes]
rs57928699	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58061761	0.91[AFR][1000 genomes]
rs60228288	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60422392	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60726022	0.83[AFR][1000 genomes]
rs60854219	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61316646	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61689863	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62095427	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62095459	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62096462	0.95[ASN][1000 genomes]
rs62096463	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62096464	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62096465	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62096466	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62096468	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096469	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096470	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096471	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096474	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096477	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62096478	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907280	0.91[AFR][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4609941	HDHD2	Cis_1M	lymphoblastoid	RTeQTL

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	chr18:44639800-44654800	Weak transcription	HMEC	breast
19	chr18:44639800-44660600	Weak transcription	NH-A	brain
20	chr18:44639800-44660800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr18:44640400-44662000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr18:44640600-44646200	Weak transcription	GM12878-XiMat	blood
23	chr18:44640600-44675600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr18:44640800-44662000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr18:44641000-44653800	Weak transcription	HSMM	muscle
26	chr18:44641000-44654200	Weak transcription	Brain Anterior Caudate	brain
27	chr18:44641000-44654800	Weak transcription	Hela-S3	cervix
28	chr18:44641200-44654200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr18:44641200-44655600	Weak transcription	Fetal Brain Female	brain
30	chr18:44641200-44659600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr18:44641600-44645800	Weak transcription	Fetal Lung	lung
32	chr18:44641600-44654000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr18:44641600-44654200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr18:44641600-44654200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr18:44641600-44660400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr18:44641600-44670400	Weak transcription	HepG2	liver
37	chr18:44641600-44674000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr18:44641600-44675800	Weak transcription	Lung	lung
39	chr18:44641800-44646200	Weak transcription	Fetal Intestine Large	intestine
40	chr18:44641800-44649600	Weak transcription	Right Ventricle	heart
41	chr18:44641800-44649800	Weak transcription	Dnd41	blood
42	chr18:44641800-44650800	Weak transcription	Fetal Stomach	stomach
43	chr18:44641800-44652400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr18:44641800-44653600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr18:44641800-44653600	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr18:44641800-44653800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr18:44641800-44653800	Weak transcription	Left Ventricle	heart
48	chr18:44641800-44654000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr18:44641800-44655000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr18:44641800-44655800	Weak transcription	Brain Cingulate Gyrus	brain

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