Variant report

Variant	rs3809966
Chromosome Location	chr18:44677627-44677628
allele	C/T
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	POLR2A	chr18:44674722-44678085	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr18:44676088-44677761	HCT-116	colon:	n/a	n/a
3	POLR2A	chr18:44675606-44678049	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr18:44676178-44677904	U87	brain:	n/a	n/a
5	POLR2A	chr18:44676357-44677781	GM12891	blood:	n/a	n/a
6	RELA	chr18:44676262-44677801	GM18951	blood:	n/a	chr18:44676928-44676937 chr18:44676928-44676937
7	GABPA	chr18:44676071-44677636	MCF-7	breast:	n/a	chr18:44676547-44676558 chr18:44676547-44676556 chr18:44676547-44676561 chr18:44676544-44676558
8	POLR2A	chr18:44677374-44677844	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr18:44675802-44678239	K562	blood:	n/a	n/a
10	POLR2A	chr18:44675895-44678712	Hela-S3	cervix:	n/a	n/a
11	KAP1	chr18:44676221-44677663	HEK293	kidney:	n/a	n/a
12	RCOR1	chr18:44677561-44678304	K562	blood:	n/a	n/a
13	POLR2A	chr18:44675788-44678010	K562	blood:	n/a	n/a
14	POLR2A	chr18:44677437-44677902	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr18:44676304-44677778	SK-N-SH	brain:	n/a	n/a
16	FOXA1	chr18:44677303-44677778	HepG2	liver:	n/a	chr18:44677550-44677565
17	POLR2A	chr18:44676296-44677819	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr18:44676315-44677788	GM12878	blood:	n/a	n/a
19	POLR2A	chr18:44677418-44677749	GM12891	blood:	n/a	n/a
20	GTF2F1	chr18:44677592-44677636	K562	blood:	n/a	n/a
21	POLR2A	chr18:44676268-44677854	Hela-S3	cervix:	n/a	n/a
22	FOXA2	chr18:44677396-44677653	HepG2	liver:	n/a	n/a
23	EP300	chr18:44677606-44678185	K562	blood:	n/a	n/a
24	POLR2A	chr18:44675844-44678064	HepG2	liver:	n/a	n/a
25	POLR2A	chr18:44675504-44677796	K562	blood:	n/a	n/a
26	HCFC1	chr18:44675984-44678219	Hela-S3	cervix:	n/a	n/a
27	MXI1	chr18:44675604-44677907	IMR90	lung:	n/a	n/a
28	MAX	chr18:44675900-44677801	NB4	blood:	n/a	n/a
29	POLR2A	chr18:44675920-44677723	K562	blood:	n/a	n/a
30	POLR2A	chr18:44676155-44677921	HL-60	blood:	n/a	n/a
31	POLR2A	chr18:44675835-44678191	HepG2	liver:	n/a	n/a
32	POLR2A	chr18:44675620-44679012	K562	blood:	n/a	n/a
33	POLR2A	chr18:44676131-44677948	HUVEC	blood vessel:	n/a	n/a
34	MTA3	chr18:44676167-44678351	GM12878	blood:	n/a	n/a
35	POLR2A	chr18:44675563-44678591	HepG2	liver:	n/a	n/a
36	POLR2A	chr18:44675781-44678046	K562	blood:	n/a	n/a
37	POLR2A	chr18:44676076-44677964	PBDE	blood:	n/a	n/a
38	TAL1	chr18:44676784-44678290	K562	blood:	n/a	chr18:44677746-44677755
39	USF2	chr18:44677208-44677840	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr18:44675922-44677812	Raji	blood:	n/a	n/a
41	POLR2A	chr18:44676271-44677729	HEK293	kidney:	n/a	n/a
42	MTA3	chr18:44676878-44677643	GM12878	blood:	n/a	n/a
43	POLR2A	chr18:44675752-44678143	K562	blood:	n/a	n/a
44	TBP	chr18:44676372-44678167	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr18:44675842-44678055	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr18:44675797-44678749	GM12878	blood:	n/a	n/a
47	MAX	chr18:44676263-44677727	Hela-S3	cervix:	n/a	n/a
48	RELA	chr18:44676171-44677869	GM18505	blood:	n/a	chr18:44676928-44676937 chr18:44676928-44676937
49	TBP	chr18:44677564-44677654	K562	blood:	n/a	n/a
50	POLR2A	chr18:44675591-44678820	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:44675848..44678361-chr18:44699497..44704011,6	MCF-7	breast:
2	chr18:44675372..44679287-chr18:44700113..44704114,10	MCF-7	breast:
3	chr18:44676902..44678518-chr18:44699803..44701757,2	K562	blood:
4	chr18:44660900..44663835-chr18:44675479..44677959,3	MCF-7	breast:

Variant related genes	Relation type
HDHD2	TF binding region
ENSG00000134049	Chromatin interaction
ENSG00000267228	Chromatin interaction
ENSG00000267800	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10083937	1.00[CEU][hapmap];0.82[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];1.00[ASN][1000 genomes]
rs10520715	0.81[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs11082563	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11082564	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11082566	0.80[ASN][1000 genomes]
rs11872531	0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11873315	0.80[ASN][1000 genomes]
rs11873812	0.80[ASN][1000 genomes]
rs11873880	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11874862	0.83[ASN][1000 genomes]
rs11875558	0.83[ASN][1000 genomes]
rs11875768	0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[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];0.91[AFR][1000 genomes]
rs12326221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12326412	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];1.00[ASN][1000 genomes]
rs12326457	1.00[CEU][hapmap];0.92[JPT][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]
rs12326465	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]
rs12386076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12386092	1.00[CEU][hapmap];0.81[CHB][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	1.00[ASW][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap]
rs1434528	1.00[ASW][hapmap];0.85[GIH][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs16948914	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][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]
rs16948928	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]
rs16949157	1.00[CEU][hapmap];0.86[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];1.00[ASN][1000 genomes]
rs16949275	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]
rs16950217	0.85[CEU][hapmap]
rs16952848	0.85[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs16958432	1.00[ASW][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs16958440	0.85[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs16958699	1.00[AFR][1000 genomes]
rs16958701	1.00[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	0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17784795	0.81[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs17784867	0.80[ASN][1000 genomes]
rs2117373	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][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];0.96[EUR][1000 genomes]
rs2289130	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2289131	1.00[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2289132	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][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];1.00[ASN][1000 genomes]
rs28587821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809965	1.00[CEU][hapmap];0.81[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];1.00[ASN][1000 genomes]
rs4609941	0.91[AFR][1000 genomes]
rs56395942	1.00[AFR][1000 genomes]
rs57744138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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];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	1.00[AFR][1000 genomes]
rs60422392	1.00[AFR][1000 genomes]
rs60726022	0.91[AFR][1000 genomes];0.97[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];0.97[ASN][1000 genomes]
rs72909237	0.83[ASN][1000 genomes]
rs72909248	0.83[ASN][1000 genomes]
rs998818	0.83[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3809966	HDHD2	cis	lymphoblastoid	seeQTL
rs3809966	HDHD2	Cis_1M	lymphoblastoid	RTeQTL
rs3809966	HDHD2	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44675000-44678000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr18:44675400-44678200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr18:44675800-44677800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr18:44675800-44677800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr18:44675800-44678200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr18:44676000-44677800	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr18:44676000-44678000	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr18:44676000-44678000	Active TSS	Fetal Brain Female	brain
9	chr18:44676000-44678000	Active TSS	HSMM	muscle
10	chr18:44676200-44677800	Active TSS	Fetal Muscle Trunk	muscle
11	chr18:44676200-44678000	Active TSS	Thymus	Thymus
12	chr18:44676200-44678000	Active TSS	GM12878-XiMat	blood
13	chr18:44676800-44677800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr18:44677000-44677800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr18:44677000-44677800	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr18:44677000-44677800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr18:44677000-44677800	Flanking Active TSS	HUVEC	blood vessel
18	chr18:44677000-44678000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr18:44677000-44678000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr18:44677000-44678000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr18:44677000-44678000	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr18:44677200-44677800	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr18:44677200-44677800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr18:44677200-44677800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr18:44677200-44677800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr18:44677200-44677800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr18:44677200-44677800	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr18:44677200-44677800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr18:44677200-44677800	Flanking Active TSS	Fetal Lung	lung
30	chr18:44677200-44677800	Flanking Active TSS	Rectal Smooth Muscle	rectum
31	chr18:44677200-44677800	Flanking Active TSS	K562	blood
32	chr18:44677200-44677800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr18:44677200-44677800	Flanking Active TSS	NH-A	brain
34	chr18:44677200-44677800	Flanking Active TSS	NHEK	skin
35	chr18:44677200-44677800	Flanking Active TSS	NHLF	lung
36	chr18:44677200-44678000	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr18:44677200-44678000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr18:44677200-44678000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr18:44677200-44678000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr18:44677200-44678200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr18:44677200-44678200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr18:44677400-44677800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr18:44677400-44677800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr18:44677400-44677800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr18:44677400-44677800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr18:44677400-44677800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr18:44677400-44677800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr18:44677400-44677800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr18:44677400-44677800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr18:44677400-44677800	Flanking Active TSS	Brain Cingulate Gyrus	brain

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