Variant report

Variant	rs3809965
Chromosome Location	chr18:44676872-44676873
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	POLR2A	chr18:44674722-44678085	MCF10A-Er-Src	breast:	n/a	n/a
2	REST	chr18:44676123-44677439	HL-60	blood:	n/a	n/a
3	POLR2A	chr18:44676357-44677168	HUVEC	blood vessel:	n/a	n/a
4	PBX3	chr18:44676238-44677237	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr18:44676088-44677761	HCT-116	colon:	n/a	n/a
6	RFX5	chr18:44676559-44677171	GM12878	blood:	n/a	n/a
7	CHD2	chr18:44676025-44677115	K562	blood:	n/a	chr18:44676530-44676540
8	ZNF143	chr18:44676407-44677330	GM12878	blood:	n/a	n/a
9	REST	chr18:44676742-44677037	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr18:44675606-44678049	PFSK-1	brain:	n/a	n/a
11	YY1	chr18:44676397-44677065	GM12878	blood:	n/a	n/a
12	MXI1	chr18:44676309-44677597	HepG2	liver:	n/a	n/a
13	RCOR1	chr18:44675852-44677351	K562	blood:	n/a	n/a
14	POLR2A	chr18:44676178-44677904	U87	brain:	n/a	n/a
15	MAX	chr18:44676252-44677255	MCF-7	breast:	n/a	n/a
16	TAF1	chr18:44676350-44677339	GM12878	blood:	n/a	n/a
17	CCNT2	chr18:44675920-44677117	K562	blood:	n/a	chr18:44676913-44676922
18	POLR2A	chr18:44676233-44677370	A549	lung:	n/a	n/a
19	POU2F2	chr18:44676583-44677198	GM12891	blood:	n/a	n/a
20	GABPA	chr18:44676386-44677222	A549	lung:	n/a	chr18:44676547-44676558 chr18:44676547-44676556 chr18:44676547-44676561 chr18:44676544-44676558
21	THAP1	chr18:44676803-44676951	K562	blood:	n/a	n/a
22	POLR2A	chr18:44676357-44677781	GM12891	blood:	n/a	n/a
23	RELA	chr18:44676262-44677801	GM18951	blood:	n/a	chr18:44676928-44676937 chr18:44676928-44676937
24	EGR1	chr18:44676771-44677011	GM12878	blood:	n/a	n/a
25	GABPA	chr18:44676071-44677636	MCF-7	breast:	n/a	chr18:44676547-44676558 chr18:44676547-44676556 chr18:44676547-44676561 chr18:44676544-44676558
26	TCF12	chr18:44676508-44677284	ECC-1	luminal epithelium:	n/a	n/a
27	SIN3A	chr18:44676202-44677202	GM12878	blood:	n/a	n/a
28	TCF7L2	chr18:44675932-44677072	Hela-S3	cervix:	n/a	n/a
29	BCLAF1	chr18:44676300-44677253	GM12878	blood:	n/a	chr18:44676907-44676916 chr18:44676862-44676871 chr18:44676841-44676854
30	MXI1	chr18:44676388-44677121	K562	blood:	n/a	n/a
31	CTCF	chr18:44676418-44676897	GM12878	blood:	n/a	chr18:44676645-44676658
32	ELK4	chr18:44676572-44677128	Hela-S3	cervix:	n/a	chr18:44676861-44676872
33	BRCA1	chr18:44676397-44677399	Hela-S3	cervix:	n/a	n/a
34	MAX	chr18:44676768-44677054	K562	blood:	n/a	n/a
35	ELF1	chr18:44676621-44677119	K562	blood:	n/a	chr18:44676858-44676871
36	TAF1	chr18:44676375-44677190	SK-N-SH	brain:	n/a	n/a
37	TAF1	chr18:44676677-44677051	GM12891	blood:	n/a	n/a
38	POLR2A	chr18:44675802-44678239	K562	blood:	n/a	n/a
39	RCOR1	chr18:44676461-44677362	GM12878	blood:	n/a	n/a
40	RCOR1	chr18:44676303-44677201	HepG2	liver:	n/a	n/a
41	REST	chr18:44676705-44677048	A549	lung:	n/a	n/a
42	REST	chr18:44676859-44677132	PANC-1	pancreas:	n/a	n/a
43	TBP	chr18:44676379-44677116	HepG2	liver:	n/a	n/a
44	NRF1	chr18:44675987-44677169	SK-N-SH	brain:	n/a	chr18:44676547-44676558 chr18:44676547-44676556 chr18:44676547-44676561 chr18:44676544-44676558
45	POLR2A	chr18:44676296-44677197	H1-hESC	embryonic stem cell:	n/a	n/a
46	YY1	chr18:44676540-44676933	GM12891	blood:	n/a	n/a
47	POLR2A	chr18:44676367-44677176	GM10847	blood:	n/a	n/a
48	IRF1	chr18:44675904-44677160	K562	blood:	n/a	chr18:44676909-44676923 chr18:44676904-44676918
49	POLR2A	chr18:44675895-44678712	Hela-S3	cervix:	n/a	n/a
50	TAF1	chr18:44676768-44677136	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:44676561..44677117-chr21:38445057..38446026,2	Hela-S3	cervix:
2	chr18:44675848..44678361-chr18:44699497..44704011,6	MCF-7	breast:
3	chr18:44675372..44679287-chr18:44700113..44704114,10	MCF-7	breast:
4	chr18:44660900..44663835-chr18:44675479..44677959,3	MCF-7	breast:
5	chr17:79479596..79480269-chr18:44676737..44677238,2	HCT-116	colon:
6	chr18:44676438..44677089-chr4:99849867..99850574,2	HCT-116	colon:

Variant related genes	Relation type
HDHD2	TF binding region
ENSG00000182670	Chromatin interaction
ENSG00000184009	Chromatin interaction
ENSG00000229947	Chromatin interaction
ENSG00000185808	Chromatin interaction
ENSG00000134049	Chromatin interaction
ENSG00000151247	Chromatin interaction
ENSG00000263923	Chromatin interaction
ENSG00000267800	Chromatin interaction
ENSG00000267228	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10083937	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[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];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11082563	0.87[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	0.90[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	1.00[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];0.86[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]
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];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]
rs1434528	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs16948914	1.00[CEU][hapmap];0.81[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];0.81[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];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	0.87[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs16958432	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs16958440	0.87[CEU][hapmap];0.90[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	0.90[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];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs17784867	0.80[ASN][1000 genomes]
rs2117373	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]
rs2289130	0.87[CEU][hapmap];0.81[CHB][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];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]
rs3809966	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]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3809965	HDHD2	cis	multi-tissue	Pritchard
rs3809965	HDHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 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	chr18:44675200-44677200	Active TSS	K562	blood
3	chr18:44675400-44677400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr18:44675400-44677400	Active TSS	A549	lung
5	chr18:44675400-44677600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr18:44675400-44677600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr18:44675400-44678200	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr18:44675600-44677200	Active TSS	NHLF	lung
9	chr18:44675600-44677400	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr18:44675600-44677400	Active TSS	NHDF-Ad	bronchial
11	chr18:44675600-44677600	Active TSS	H1 Cell Line	embryonic stem cell
12	chr18:44675600-44677600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr18:44675600-44677600	Active TSS	Brain Angular Gyrus	brain
14	chr18:44675600-44677600	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr18:44675800-44677000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr18:44675800-44677400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr18:44675800-44677400	Active TSS	Fetal Kidney	kidney
18	chr18:44675800-44677600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr18:44675800-44677600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr18:44675800-44677600	Active TSS	H9 Cell Line	embryonic stem cell
21	chr18:44675800-44677600	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr18:44675800-44677600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr18:44675800-44677600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr18:44675800-44677600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr18:44675800-44677600	Active TSS	Fetal Intestine Large	intestine
26	chr18:44675800-44677800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr18:44675800-44677800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr18:44675800-44678200	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr18:44676000-44677200	Active TSS	Fetal Lung	lung
30	chr18:44676000-44677200	Active TSS	Fetal Stomach	stomach
31	chr18:44676000-44677400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr18:44676000-44677400	Active TSS	Brain Hippocampus Middle	brain
33	chr18:44676000-44677400	Active TSS	Placenta Amnion	Placenta Amnion
34	chr18:44676000-44677600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr18:44676000-44677600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr18:44676000-44677600	Active TSS	Fetal Intestine Small	intestine
37	chr18:44676000-44677600	Active TSS	Ovary	ovary
38	chr18:44676000-44677600	Active TSS	Psoas Muscle	Psoas
39	chr18:44676000-44677800	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr18:44676000-44678000	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr18:44676000-44678000	Active TSS	Fetal Brain Female	brain
42	chr18:44676000-44678000	Active TSS	HSMM	muscle
43	chr18:44676200-44677200	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr18:44676200-44677200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr18:44676200-44677200	Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr18:44676200-44677200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr18:44676200-44677200	Active TSS	Duodenum Mucosa	Duodenum
48	chr18:44676200-44677200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr18:44676200-44677200	Active TSS	Rectal Smooth Muscle	rectum
50	chr18:44676200-44677200	Active TSS	NH-A	brain

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