Variant report

Variant	rs1674999
Chromosome Location	chr4:88027650-88027651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87927805..87929886-chr4:88027084..88029698,4	MCF-7	breast:
2	chr4:88026944..88029888-chr4:88036043..88037768,2	MCF-7	breast:
3	chr4:88021442..88026056-chr4:88026505..88030511,4	MCF-7	breast:
4	chr4:88013784..88016288-chr4:88023619..88027731,5	MCF-7	breast:
5	chr4:87849195..87851661-chr4:88027634..88030050,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10023050	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1037814	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11097127	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11946481	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1408	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16930	0.94[ASN][1000 genomes]
rs17012368	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2045592	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2125787	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236984	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236985	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236987	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236992	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236993	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236995	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236996	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28432336	0.84[ASN][1000 genomes]
rs28677145	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2926511	0.90[ASN][1000 genomes]
rs342435	0.94[ASN][1000 genomes]
rs342437	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342438	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342452	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342453	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342454	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342456	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342466	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342467	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342468	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342469	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736669	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3775214	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775217	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775220	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775221	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775223	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs442177	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693156	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72877984	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7660883	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9998251	0.86[AMR][1000 genomes];0.83[EUR][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

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87995200-88029200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:87995400-88037800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:88003400-88028600	Weak transcription	HSMMtube	muscle
4	chr4:88011800-88032800	Weak transcription	Colonic Mucosa	Colon
5	chr4:88015200-88028800	Weak transcription	Aorta	Aorta
6	chr4:88015200-88028800	Weak transcription	Fetal Heart	heart
7	chr4:88015200-88029200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:88015800-88035400	Weak transcription	Right Ventricle	heart
9	chr4:88018600-88029200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:88018600-88034200	Weak transcription	Fetal Stomach	stomach
11	chr4:88019000-88072200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:88021000-88029200	Weak transcription	Ovary	ovary
13	chr4:88021000-88034200	Weak transcription	Spleen	Spleen
14	chr4:88021200-88029200	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:88021600-88028800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:88021600-88029200	Weak transcription	Right Atrium	heart
17	chr4:88021600-88036600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:88021600-88037800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:88021800-88029000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:88021800-88029200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:88021800-88029400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:88021800-88036000	Weak transcription	Brain Angular Gyrus	brain
23	chr4:88023000-88028600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:88023800-88029200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:88024400-88029200	Enhancers	Fetal Intestine Large	intestine
26	chr4:88025000-88029200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr4:88025000-88031200	Strong transcription	GM12878-XiMat	blood
28	chr4:88025200-88029000	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr4:88025400-88027800	Weak transcription	Hela-S3	cervix
30	chr4:88025400-88028400	Weak transcription	HSMM	muscle
31	chr4:88025400-88028800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:88025400-88028800	Weak transcription	Brain Anterior Caudate	brain
33	chr4:88025600-88028000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:88025600-88028600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:88025600-88028600	Weak transcription	A549	lung
36	chr4:88025600-88028800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr4:88025600-88029200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:88025600-88029200	Weak transcription	Esophagus	oesophagus
39	chr4:88025600-88029200	Weak transcription	Fetal Muscle Leg	muscle
40	chr4:88025600-88029200	Weak transcription	Gastric	stomach
41	chr4:88025600-88029200	Weak transcription	Pancreas	Pancrea
42	chr4:88025600-88030200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr4:88025600-88034200	Weak transcription	Lung	lung
44	chr4:88025600-88035600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:88025600-88035800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr4:88025800-88027800	Weak transcription	NHDF-Ad	bronchial
47	chr4:88025800-88028000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr4:88025800-88028600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:88025800-88028800	Weak transcription	HMEC	breast
50	chr4:88025800-88029400	Weak transcription	Small Intestine	intestine

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