Variant report

Variant	rs442177
Chromosome Location	chr4:88030261-88030262
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:88022117..88024925-chr4:88027985..88030710,2	K562	blood:
2	chr4:87812118..87814923-chr4:88028471..88030564,2	K562	blood:
3	chr4:88024363..88026324-chr4:88027975..88030672,2	K562	blood:
4	chr4:88021442..88026056-chr4:88026505..88030511,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10023050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1037814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11097127	0.85[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs11946481	0.84[ASN][1000 genomes]
rs1408	0.92[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs1674999	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16930	0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs17012368	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2045592	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2125787	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236987	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28432336	0.84[ASN][1000 genomes]
rs28677145	0.85[ASN][1000 genomes]
rs2926511	0.95[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs342435	0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs342437	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342453	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342454	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342456	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342466	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736669	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs3775214	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775217	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3775220	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3775221	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3775223	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs447990	0.83[YRI][hapmap]
rs4693156	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs72877984	0.85[ASN][1000 genomes]
rs7660883	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs9998251	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]

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

Variant related diseases (count:3)

Disease	PMID	Source
Triglycerides	20864672	GWAS catalog
Triglycerides	24097068	GWAS catalog
Triglycerides	20686565	GWAS catalog

Chromatin state (count:124 , 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	chr4:88025600-88034200	Weak transcription	Lung	lung
12	chr4:88025600-88035600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:88025600-88035800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr4:88026200-88030600	Strong transcription	K562	blood
15	chr4:88026200-88031800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:88026200-88042200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr4:88026400-88030600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:88026400-88030600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr4:88026400-88030600	Strong transcription	Dnd41	blood
20	chr4:88026400-88031200	Strong transcription	Primary B cells from cord blood	blood
21	chr4:88026400-88042400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr4:88026400-88063600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:88026600-88030800	Strong transcription	Primary hematopoietic stem cells	blood
24	chr4:88026600-88031800	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:88026600-88031800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:88026600-88031800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:88026600-88033600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr4:88026600-88042200	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr4:88026600-88042600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr4:88026600-88055600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:88026800-88030600	Strong transcription	Thymus	Thymus
32	chr4:88026800-88031000	Strong transcription	Fetal Thymus	thymus
33	chr4:88026800-88031000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr4:88026800-88032000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:88026800-88032800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr4:88026800-88035800	Weak transcription	Brain Substantia Nigra	brain
37	chr4:88027000-88032800	Weak transcription	Fetal Kidney	kidney
38	chr4:88027000-88033000	Weak transcription	Stomach Mucosa	stomach
39	chr4:88027000-88035400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr4:88027000-88037600	Strong transcription	Liver	Liver
41	chr4:88027200-88031200	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:88027400-88030600	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr4:88028000-88030400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr4:88028000-88030800	Strong transcription	HepG2	liver
45	chr4:88028400-88035800	Weak transcription	Psoas Muscle	Psoas
46	chr4:88028600-88030400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr4:88028600-88030400	Enhancers	Muscle Satellite Cultured Cells	--
48	chr4:88028600-88030400	Genic enhancers	Adipose Nuclei	Adipose
49	chr4:88028600-88030400	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr4:88028800-88030600	Strong transcription	Fetal Lung	lung

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