Variant report

Variant	rs1408
Chromosome Location	chr4:88057353-88057354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:88056180..88057831-chr4:88140231..88142000,2	K562	blood:
2	chr4:88055050..88057902-chr4:88066373..88068330,2	K562	blood:
3	chr4:88056797..88059006-chr4:88063394..88065724,2	K562	blood:
4	chr4:88052295..88056117-chr4:88057226..88059764,4	K562	blood:
5	chr4:88055864..88059165-chr4:88060107..88062593,3	K562	blood:

Variant related genes	Relation type
ENSG00000145332	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10023050	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1037814	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11097127	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1674999	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16930	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs17012368	0.86[ASN][1000 genomes]
rs2045592	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2125787	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs236984	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236985	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236987	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236992	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236993	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs236995	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236996	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2926511	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs342435	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs342437	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs342438	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs342452	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs342453	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs342454	0.92[CEU][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs342456	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs342466	0.93[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs342467	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs342468	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs342469	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3736669	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3775214	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3775217	0.89[ASN][1000 genomes]
rs3775220	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs3775221	0.89[ASN][1000 genomes]
rs3775223	0.89[ASN][1000 genomes]
rs442177	0.92[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs4693156	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs7660883	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs9998251	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88019000-88072200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:88026400-88063600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:88030600-88057600	Weak transcription	Brain Germinal Matrix	brain
4	chr4:88032800-88059000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr4:88035600-88063800	Strong transcription	Primary T cells from cord blood	blood
6	chr4:88036400-88063600	Weak transcription	Fetal Brain Male	brain
7	chr4:88036800-88059200	Weak transcription	Fetal Brain Female	brain
8	chr4:88042800-88069400	Strong transcription	Placenta	Placenta
9	chr4:88043000-88061400	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr4:88043400-88064800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:88043600-88064600	Strong transcription	GM12878-XiMat	blood
12	chr4:88044400-88060800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:88044600-88059200	Strong transcription	Primary B cells from peripheral blood	blood
14	chr4:88044600-88060200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr4:88044600-88061400	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr4:88044600-88061600	Strong transcription	Fetal Intestine Large	intestine
17	chr4:88044600-88062200	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr4:88044600-88067600	Strong transcription	Primary B cells from cord blood	blood
19	chr4:88044800-88059400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr4:88044800-88061400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr4:88044800-88061600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr4:88045000-88060400	Strong transcription	Primary hematopoietic stem cells	blood
23	chr4:88045200-88057800	Strong transcription	HUVEC	blood vessel
24	chr4:88045600-88057600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:88045600-88058800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:88045600-88059200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:88045600-88059600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:88045600-88060400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:88045600-88063800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:88045600-88063800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:88045800-88058200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:88045800-88059200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:88045800-88059800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr4:88045800-88061200	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr4:88045800-88061400	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr4:88045800-88063000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:88045800-88067600	Strong transcription	Fetal Thymus	thymus
38	chr4:88046000-88058400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr4:88046000-88058600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:88046000-88059000	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr4:88046000-88059200	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:88046000-88059400	Strong transcription	Dnd41	blood
43	chr4:88046000-88061400	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr4:88046200-88058200	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr4:88046200-88058600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:88046200-88059200	Strong transcription	Ovary	ovary
47	chr4:88046200-88059800	Strong transcription	Fetal Lung	lung
48	chr4:88046200-88061200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr4:88046200-88061400	Strong transcription	Adipose Nuclei	Adipose
50	chr4:88046200-88061400	Strong transcription	Stomach Smooth Muscle	stomach

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