Variant report

Variant	rs3733377
Chromosome Location	chr4:88029482-88029483
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:87927805..87929886-chr4:88027084..88029698,4	MCF-7	breast:
2	chr4:88022117..88024925-chr4:88027985..88030710,2	K562	blood:
3	chr4:87812118..87814923-chr4:88028471..88030564,2	K562	blood:
4	chr4:88024363..88026324-chr4:88027975..88030672,2	K562	blood:
5	chr4:88026944..88029888-chr4:88036043..88037768,2	MCF-7	breast:
6	chr4:88021442..88026056-chr4:88026505..88030511,4	MCF-7	breast:
7	chr4:88027865..88029794-chr4:88040230..88042955,3	MCF-7	breast:
8	chr4:87849195..87851661-chr4:88027634..88030050,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10018904	0.86[ASN][1000 genomes]
rs10023056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10029915	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10032710	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10516788	0.90[CEU][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap]
rs13120301	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1481947	0.84[MEX][hapmap]
rs151450	0.97[ASN][1000 genomes]
rs151451	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552144	0.83[MEX][hapmap]
rs17012234	0.90[CEU][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap]
rs17012334	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs17012512	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17605615	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17668131	0.86[ASN][1000 genomes]
rs17701999	0.90[CEU][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap]
rs17752307	0.90[CEU][hapmap]
rs1842685	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2035403	0.99[ASN][1000 genomes]
rs2061498	0.92[EUR][1000 genomes]
rs2280952	0.86[ASN][1000 genomes]
rs2280954	0.81[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs236676	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236679	0.86[ASN][1000 genomes]
rs236681	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3193672	0.84[MEX][hapmap]
rs3736668	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3755980	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3755983	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3755985	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775209	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775211	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775226	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775228	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4577539	0.84[MEX][hapmap]
rs4693802	0.87[GIH][hapmap]
rs55982755	0.92[EUR][1000 genomes]
rs60695258	0.99[ASN][1000 genomes]
rs66477840	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6819155	0.90[CEU][hapmap];0.94[GIH][hapmap];0.81[TSI][hapmap]
rs6840258	0.89[CEU][hapmap]
rs6854749	0.90[CEU][hapmap]
rs7665282	0.90[CEU][hapmap]
rs767315	0.89[CEU][hapmap]
rs7682652	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3733377	HSD17B13	cis	multi-tissue	Pritchard
rs3733377	HERC6	cis	parietal	SCAN
rs3733377	HSD17B13	cis	parietal	SCAN
rs3733377	SLC10A6	cis	cerebellum	SCAN
rs3733377	HSD17B13	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87995400-88037800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:88011800-88032800	Weak transcription	Colonic Mucosa	Colon
3	chr4:88015800-88035400	Weak transcription	Right Ventricle	heart
4	chr4:88018600-88034200	Weak transcription	Fetal Stomach	stomach
5	chr4:88019000-88072200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:88021000-88034200	Weak transcription	Spleen	Spleen
7	chr4:88021600-88036600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:88021600-88037800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:88021800-88036000	Weak transcription	Brain Angular Gyrus	brain
10	chr4:88025000-88031200	Strong transcription	GM12878-XiMat	blood
11	chr4:88025600-88030200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr4:88025600-88034200	Weak transcription	Lung	lung
13	chr4:88025600-88035600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:88025600-88035800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr4:88026200-88030600	Strong transcription	K562	blood
16	chr4:88026200-88031800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:88026200-88042200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr4:88026400-88030600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:88026400-88030600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr4:88026400-88030600	Strong transcription	Dnd41	blood
21	chr4:88026400-88031200	Strong transcription	Primary B cells from cord blood	blood
22	chr4:88026400-88042400	Strong transcription	Primary B cells from peripheral blood	blood
23	chr4:88026400-88063600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:88026600-88030800	Strong transcription	Primary hematopoietic stem cells	blood
25	chr4:88026600-88031800	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:88026600-88031800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:88026600-88031800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:88026600-88033600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr4:88026600-88042200	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr4:88026600-88042600	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr4:88026600-88055600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr4:88026800-88030600	Strong transcription	Thymus	Thymus
33	chr4:88026800-88031000	Strong transcription	Fetal Thymus	thymus
34	chr4:88026800-88031000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr4:88026800-88032000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:88026800-88032800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:88026800-88035800	Weak transcription	Brain Substantia Nigra	brain
38	chr4:88027000-88029600	Genic enhancers	Fetal Intestine Small	intestine
39	chr4:88027000-88032800	Weak transcription	Fetal Kidney	kidney
40	chr4:88027000-88033000	Weak transcription	Stomach Mucosa	stomach
41	chr4:88027000-88035400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr4:88027000-88037600	Strong transcription	Liver	Liver
43	chr4:88027200-88031200	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr4:88027400-88030000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr4:88027400-88030600	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr4:88028000-88030400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr4:88028000-88030800	Strong transcription	HepG2	liver
48	chr4:88028400-88030200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:88028400-88030200	Enhancers	Osteobl	bone
50	chr4:88028400-88035800	Weak transcription	Psoas Muscle	Psoas

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