Variant report

Variant	rs3775221
Chromosome Location	chr4:88011793-88011794
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:88011101..88013841-chr4:88036538..88039018,2	MCF-7	breast:
2	chr4:88004411..88007536-chr4:88008930..88011901,3	K562	blood:
3	chr4:87946215..87948894-chr4:88011118..88013120,2	MCF-7	breast:
4	chr4:87855131..87857677-chr4:88011511..88016191,4	MCF-7	breast:
5	chr4:87988554..87990336-chr4:88011051..88012696,2	K562	blood:

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10023050	0.89[ASN][1000 genomes]
rs1037814	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11097127	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11946481	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1408	0.89[ASN][1000 genomes]
rs1674999	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16930	0.93[ASN][1000 genomes]
rs17012368	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2045592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125787	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs236984	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236985	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236987	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236992	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236993	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236995	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236996	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28432336	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28677145	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2926511	0.90[ASN][1000 genomes]
rs342435	0.93[ASN][1000 genomes]
rs342437	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342438	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342452	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342453	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342454	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342456	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342466	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs342467	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs342468	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs342469	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736669	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3775214	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775223	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442177	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4693156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877984	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7660883	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9998251	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
6	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription 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	25 gene(s)	inside rSNPs	diseases
7	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
8	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:118 , 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	chr4:87995800-88023800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:87996800-88023600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr4:88000400-88020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:88000600-88013000	Weak transcription	A549	lung
7	chr4:88001400-88013800	Weak transcription	HSMM	muscle
8	chr4:88001400-88025200	Weak transcription	Fetal Muscle Leg	muscle
9	chr4:88001600-88014000	Weak transcription	Small Intestine	intestine
10	chr4:88001800-88011800	Weak transcription	Fetal Stomach	stomach
11	chr4:88001800-88013200	Weak transcription	Stomach Mucosa	stomach
12	chr4:88001800-88013400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr4:88001800-88013800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:88001800-88025200	Weak transcription	Gastric	stomach
15	chr4:88003400-88028600	Weak transcription	HSMMtube	muscle
16	chr4:88003600-88013000	Weak transcription	HMEC	breast
17	chr4:88003600-88013200	Weak transcription	Osteobl	bone
18	chr4:88004200-88019200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr4:88004400-88025200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:88005000-88017400	Strong transcription	Dnd41	blood
21	chr4:88005800-88014000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:88007600-88014400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:88007600-88018200	Weak transcription	Thymus	Thymus
24	chr4:88008400-88013200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:88008600-88014000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:88008600-88014000	Weak transcription	Aorta	Aorta
27	chr4:88008800-88013200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr4:88008800-88014000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:88008800-88014000	Weak transcription	NHLF	lung
30	chr4:88008800-88014200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:88008800-88015000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:88009000-88013400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr4:88009000-88013600	Weak transcription	Fetal Heart	heart
34	chr4:88009000-88017800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr4:88009400-88013600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr4:88009400-88013600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr4:88009400-88013800	Weak transcription	Primary T cells from cord blood	blood
38	chr4:88009400-88017600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr4:88009600-88011800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr4:88009600-88012000	Strong transcription	GM12878-XiMat	blood
41	chr4:88009600-88013200	Weak transcription	Psoas Muscle	Psoas
42	chr4:88009600-88013400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:88009600-88013800	Weak transcription	Brain Angular Gyrus	brain
44	chr4:88009600-88013800	Weak transcription	Brain Anterior Caudate	brain
45	chr4:88009800-88013200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:88009800-88013200	Weak transcription	Brain Hippocampus Middle	brain
47	chr4:88009800-88013200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr4:88009800-88013200	Weak transcription	NHEK	skin
49	chr4:88009800-88014000	Strong transcription	Placenta	Placenta
50	chr4:88010200-88012000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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