Variant report

Variant	rs12326465
Chromosome Location	chr18:44678645-44678646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr18:44677648-44678806	K562	blood:	n/a	n/a
2	POLR2A	chr18:44675895-44678712	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr18:44675620-44679012	K562	blood:	n/a	n/a
4	POLR2A	chr18:44675797-44678749	GM12878	blood:	n/a	n/a
5	POLR2A	chr18:44675591-44678820	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr18:44678500-44681193	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:44675372..44679287-chr18:44700113..44704114,10	MCF-7	breast:

Variant related genes	Relation type
HDHD2	TF binding region
ENSG00000134049	Chromatin interaction
ENSG00000267228	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10083937	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520715	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11082563	0.90[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11082564	0.81[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11082566	0.80[ASN][1000 genomes]
rs11872531	0.89[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11873315	0.80[ASN][1000 genomes]
rs11873812	0.80[ASN][1000 genomes]
rs11873880	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11874862	0.83[ASN][1000 genomes]
rs11875558	0.83[ASN][1000 genomes]
rs11875768	1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11877644	0.83[ASN][1000 genomes]
rs11877745	0.83[ASN][1000 genomes]
rs12326122	1.00[YRI][hapmap]
rs12326221	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12326412	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];1.00[ASN][1000 genomes]
rs12326457	0.86[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];1.00[ASN][1000 genomes]
rs12386076	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12386092	0.90[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12386097	0.84[AFR][1000 genomes]
rs13547	0.81[CHB][hapmap]
rs1434528	0.81[CHB][hapmap]
rs16948914	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]
rs16948928	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]
rs16949157	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];1.00[ASN][1000 genomes]
rs16949275	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]
rs16950217	0.82[CEU][hapmap]
rs16952848	1.00[YRI][hapmap]
rs16958432	0.81[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs16958440	0.90[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs16958699	0.84[AFR][1000 genomes]
rs16958701	0.84[AFR][1000 genomes]
rs17711764	0.83[ASN][1000 genomes]
rs17712105	0.80[ASN][1000 genomes]
rs17712141	0.80[ASN][1000 genomes]
rs17712249	0.80[ASN][1000 genomes]
rs17784414	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17784795	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs17784867	0.80[ASN][1000 genomes]
rs2117373	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2289130	0.90[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2289131	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs2289132	0.82[CEU][hapmap];0.84[AFR][1000 genomes]
rs28578518	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587821	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809965	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];1.00[ASN][1000 genomes]
rs3809966	1.00[CEU][hapmap];0.90[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];1.00[ASN][1000 genomes]
rs56395942	0.84[AFR][1000 genomes]
rs57744138	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57928699	0.84[AFR][1000 genomes]
rs58061761	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58715341	0.95[ASN][1000 genomes]
rs59217333	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60228288	0.84[AFR][1000 genomes]
rs60422392	0.84[AFR][1000 genomes]
rs60726022	0.97[ASN][1000 genomes]
rs60854219	0.84[AFR][1000 genomes]
rs61316646	0.84[AFR][1000 genomes]
rs61689863	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62095459	0.80[AFR][1000 genomes]
rs62096463	0.84[AFR][1000 genomes]
rs62096464	0.84[AFR][1000 genomes]
rs62096465	0.84[AFR][1000 genomes]
rs62096466	0.84[AFR][1000 genomes]
rs62096469	0.84[AFR][1000 genomes]
rs62096470	0.84[AFR][1000 genomes]
rs62096471	0.84[AFR][1000 genomes]
rs62096474	0.84[AFR][1000 genomes]
rs62096477	0.84[AFR][1000 genomes]
rs62096478	0.84[AFR][1000 genomes]
rs72907280	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs72909237	0.83[ASN][1000 genomes]
rs72909248	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
rs12326465	HDHD2	Cis_1M	lymphoblastoid	RTeQTL
rs12326465	HDHD2	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44677600-44680200	Weak transcription	Fetal Intestine Large	intestine
2	chr18:44677600-44685400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr18:44677600-44700200	Weak transcription	Aorta	Aorta
4	chr18:44677800-44678800	Enhancers	Fetal Heart	heart
5	chr18:44677800-44678800	Enhancers	K562	blood
6	chr18:44677800-44679400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr18:44677800-44679400	Weak transcription	NH-A	brain
8	chr18:44677800-44680000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr18:44677800-44680000	Weak transcription	Placenta	Placenta
10	chr18:44677800-44680200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr18:44677800-44680200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr18:44677800-44680400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr18:44677800-44680400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr18:44677800-44680400	Weak transcription	Fetal Thymus	thymus
15	chr18:44677800-44680400	Weak transcription	Ovary	ovary
16	chr18:44677800-44680400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr18:44677800-44680400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr18:44677800-44680600	Weak transcription	HMEC	breast
19	chr18:44677800-44680800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr18:44677800-44681000	Weak transcription	Brain Germinal Matrix	brain
21	chr18:44677800-44682800	Weak transcription	Colonic Mucosa	Colon
22	chr18:44677800-44684800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr18:44677800-44685600	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr18:44677800-44686400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr18:44677800-44686600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr18:44677800-44686600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr18:44677800-44689800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr18:44677800-44693400	Weak transcription	Gastric	stomach
29	chr18:44677800-44698200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr18:44677800-44699000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr18:44677800-44700400	Weak transcription	Spleen	Spleen
32	chr18:44677800-44701000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr18:44677800-44701000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr18:44677800-44701000	Weak transcription	A549	lung
35	chr18:44677800-44701800	Weak transcription	Esophagus	oesophagus
36	chr18:44678000-44679000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr18:44678000-44679400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr18:44678000-44679400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr18:44678000-44679400	Weak transcription	HSMM	muscle
40	chr18:44678000-44680000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr18:44678000-44680000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr18:44678000-44680000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr18:44678000-44680200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr18:44678000-44680200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr18:44678000-44680200	Weak transcription	Fetal Kidney	kidney
46	chr18:44678000-44680200	Weak transcription	Osteobl	bone
47	chr18:44678000-44680400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr18:44678000-44680400	Weak transcription	Primary B cells from cord blood	blood
49	chr18:44678000-44680400	Weak transcription	Brain Anterior Caudate	brain
50	chr18:44678000-44680400	Weak transcription	Duodenum Mucosa	Duodenum

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