Variant report

Variant	rs26180
Chromosome Location	chr5:118788196-118788197
allele	A/C/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	MAFK	chr5:118787982-118788443	K562	blood:	n/a	n/a
2	EGR1	chr5:118787965-118788499	MCF-7	breast:	n/a	chr5:118788193-118788207 chr5:118788346-118788356 chr5:118788097-118788121 chr5:118788177-118788191
3	BHLHE40	chr5:118787790-118788659	K562	blood:	n/a	n/a
4	POLR2A	chr5:118788092-118788565	GM12878	blood:	n/a	n/a
5	ZMIZ1	chr5:118787887-118789066	K562	blood:	n/a	n/a
6	TAF7	chr5:118788051-118788693	H1-hESC	embryonic stem cell:	n/a	n/a
7	NRF1	chr5:118788075-118788607	GM12878	blood:	n/a	chr5:118788401-118788412
8	POLR2A	chr5:118787975-118788675	MCF-7	breast:	n/a	n/a
9	SIX5	chr5:118787889-118788327	GM12878	blood:	n/a	chr5:118788096-118788110 chr5:118788100-118788109 chr5:118788098-118788107
10	JUND	chr5:118787927-118788809	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr5:118787994-118788661	A549	lung:	n/a	n/a
12	POLR2A	chr5:118788052-118788666	GM12891	blood:	n/a	n/a
13	TBP	chr5:118787892-118788645	Hela-S3	cervix:	n/a	n/a
14	POU2F2	chr5:118788091-118788633	GM12891	blood:	n/a	n/a
15	HEY1	chr5:118788051-118788589	K562	blood:	n/a	n/a
16	JUND	chr5:118787983-118788430	A549	lung:	n/a	n/a
17	HEY1	chr5:118787982-118788617	K562	blood:	n/a	n/a
18	SMC3	chr5:118787920-118788870	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr5:118787907-118788596	K562	blood:	n/a	n/a
20	MAX	chr5:118788066-118788649	GM12878	blood:	n/a	n/a
21	POLR2A	chr5:118787917-118788684	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr5:118788015-118789066	K562	blood:	n/a	n/a
23	FOS	chr5:118788023-118788292	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr5:118787894-118788776	Hela-S3	cervix:	n/a	n/a
25	TCF7L2	chr5:118788043-118789030	Hela-S3	cervix:	n/a	n/a
26	SP1	chr5:118787864-118788560	A549	lung:	n/a	chr5:118788437-118788448
27	SIX5	chr5:118787841-118788499	A549	lung:	n/a	chr5:118788096-118788110 chr5:118788100-118788109 chr5:118788098-118788107
28	TBL1XR1	chr5:118787925-118788207	K562	blood:	n/a	n/a
29	MAX	chr5:118787855-118788619	A549	lung:	n/a	n/a
30	YY1	chr5:118787810-118788471	H1-hESC	embryonic stem cell:	n/a	chr5:118788038-118788060
31	POLR2A	chr5:118787887-118788719	HCT-116	colon:	n/a	n/a
32	ZNF143	chr5:118787785-118788747	GM12878	blood:	n/a	chr5:118788098-118788116 chr5:118788102-118788121 chr5:118788100-118788109 chr5:118788098-118788107 chr5:118788719-118788729
33	MAX	chr5:118787889-118788498	SK-N-SH	brain:	n/a	n/a
34	ZNF263	chr5:118787940-118788639	HEK293-T-REx	kidney:	n/a	n/a
35	CREB1	chr5:118787864-118789123	HepG2	liver:	n/a	n/a
36	SIX5	chr5:118787910-118788317	K562	blood:	n/a	chr5:118788096-118788110 chr5:118788100-118788109 chr5:118788098-118788107
37	NFIC	chr5:118787982-118788695	ECC-1	luminal epithelium:	n/a	n/a
38	SIN3AK20	chr5:118788131-118788363	HepG2	liver:	n/a	n/a
39	TCF7L2	chr5:118787998-118788697	HCT-116	colon:	n/a	n/a
40	POLR2A	chr5:118787809-118789070	HepG2	liver:	n/a	n/a
41	POLR2A	chr5:118787988-118788485	K562	blood:	n/a	n/a
42	PML	chr5:118787867-118788807	GM12878	blood:	n/a	n/a
43	YY1	chr5:118787796-118788511	SK-N-SH_RA	brain:	n/a	chr5:118788038-118788060
44	GATA3	chr5:118788116-118788961	MCF-7	breast:	n/a	chr5:118788628-118788637 chr5:118788628-118788635 chr5:118788847-118788859 chr5:118788627-118788637 chr5:118788627-118788635
45	POLR2A	chr5:118788064-118788599	HUVEC	blood vessel:	n/a	n/a
46	FOS	chr5:118788076-118788265	MCF10A-Er-Src	breast:	n/a	n/a
47	CHD2	chr5:118787988-118788703	H1-hESC	embryonic stem cell:	n/a	n/a
48	SIN3A	chr5:118788189-118788781	GM12878	blood:	n/a	n/a
49	STAT3	chr5:118788005-118788263	MCF10A-Er-Src	breast:	n/a	n/a
50	GATA1	chr5:118788092-118789851	PBDE	blood:	n/a	chr5:118788628-118788637 chr5:118788628-118788635 chr5:118788847-118788859 chr5:118788627-118788637

No.	Distal block	Cell Line	Cell type
1	chr5:118323861..118326778-chr5:118787539..118789741,2	MCF-7	breast:
2	chr5:118787302..118789344-chr5:118814419..118817189,2	K562	blood:
3	chr22:50354001..50354626-chr5:118788080..118788710,2	HCT-116	colon:
4	chr14:50359666..50360334-chr5:118787719..118788333,2	Hela-S3	cervix:
5	chr5:118787954..118788514-chr5:172197674..172198421,2	Hela-S3	cervix:

Variant related genes	Relation type
HSD17B4	TF binding region
ENSG00000169570	Chromatin interaction
ENSG00000133835	Chromatin interaction
ENSG00000165527	Chromatin interaction
ENSG00000198355	Chromatin interaction
ENSG00000120129	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12656474	0.82[CHB][hapmap]
rs2259347	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2287712	0.83[JPT][hapmap]
rs2451816	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2546210	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs25640	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs257970	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs257972	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs257973	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs257974	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs257975	0.84[ASN][1000 genomes]
rs2945327	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs32658	0.81[CHB][hapmap]
rs32659	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs32662	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs32665	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3850200	0.83[JPT][hapmap]
rs455949	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs457106	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs461108	0.91[CHB][hapmap]
rs463098	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs465091	0.91[CHB][hapmap]
rs4895372	0.91[CHB][hapmap]
rs6875595	0.91[CHB][hapmap]
rs7721602	0.95[CHB][hapmap]

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	nsv1030717	chr5:118709310-118836951	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv4974	chr5:118750259-118795376	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs26180	HSD17B4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118786000-118788200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:118787200-118788200	Flanking Active TSS	Dnd41	blood
3	chr5:118787200-118789000	Active TSS	Brain Anterior Caudate	brain
4	chr5:118787400-118789200	Active TSS	Brain Hippocampus Middle	brain
5	chr5:118787400-118789400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr5:118787600-118788200	Weak transcription	Lung	lung
7	chr5:118787600-118788800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:118787600-118788800	Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr5:118787600-118788800	Active TSS	Brain Cingulate Gyrus	brain
10	chr5:118787600-118789000	Active TSS	Brain Angular Gyrus	brain
11	chr5:118787600-118789000	Active TSS	Fetal Heart	heart
12	chr5:118787600-118789200	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr5:118787600-118789200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:118787600-118789200	Active TSS	Brain Substantia Nigra	brain
15	chr5:118787600-118789200	Active TSS	NHEK	skin
16	chr5:118787800-118788200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr5:118787800-118788200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:118787800-118788200	Flanking Active TSS	Primary B cells from peripheral blood	blood
19	chr5:118787800-118788200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr5:118787800-118788200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:118787800-118788200	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr5:118787800-118788200	Active TSS	Fetal Brain Female	brain
23	chr5:118787800-118788200	Flanking Active TSS	Fetal Thymus	thymus
24	chr5:118787800-118788200	Active TSS	Right Atrium	heart
25	chr5:118787800-118788200	Enhancers	Stomach Mucosa	stomach
26	chr5:118787800-118788400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:118787800-118788400	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr5:118787800-118788600	Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr5:118787800-118788600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:118787800-118788800	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr5:118787800-118788800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:118787800-118788800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr5:118787800-118788800	Active TSS	Fetal Intestine Large	intestine
34	chr5:118787800-118788800	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr5:118787800-118789000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:118787800-118789000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:118787800-118789000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:118787800-118789000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:118787800-118789000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr5:118787800-118789000	Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr5:118787800-118789000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr5:118787800-118789000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:118787800-118789000	Active TSS	Duodenum Mucosa	Duodenum
44	chr5:118787800-118789000	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr5:118787800-118789000	Active TSS	Fetal Kidney	kidney
46	chr5:118787800-118789000	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr5:118787800-118789000	Active TSS	Fetal Lung	lung
48	chr5:118787800-118789000	Active TSS	Fetal Muscle Trunk	muscle
49	chr5:118787800-118789000	Active TSS	Ovary	ovary
50	chr5:118787800-118789000	Active TSS	Rectal Mucosa Donor 29	rectum

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