Variant report

Variant	rs342468
Chromosome Location	chr4:88051908-88051909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87926672..87928697-chr4:88050565..88052466,3	K562	blood:
2	chr4:88047828..88050519-chr4:88051354..88053008,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172493	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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1037814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097127	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1408	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]
rs1674999	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16930	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs17012368	0.88[ASN][1000 genomes]
rs2045592	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2125787	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs236985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs236987	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs236992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs236993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs236995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs236996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2926511	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs342435	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs342437	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs342438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs342452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342453	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342454	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342456	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3736669	0.85[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs3775214	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3775217	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775220	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775221	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775223	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs442177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4693156	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7660883	0.84[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap]
rs9998251	0.82[EUR][1000 genomes];0.91[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:126 , 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	chr4:88026600-88055600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:88030600-88057600	Weak transcription	Brain Germinal Matrix	brain
5	chr4:88032800-88059000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr4:88035600-88056800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:88035600-88063800	Strong transcription	Primary T cells from cord blood	blood
8	chr4:88036400-88063600	Weak transcription	Fetal Brain Male	brain
9	chr4:88036800-88059200	Weak transcription	Fetal Brain Female	brain
10	chr4:88040000-88052000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:88042800-88069400	Strong transcription	Placenta	Placenta
12	chr4:88043000-88061400	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr4:88043400-88064800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:88043600-88064600	Strong transcription	GM12878-XiMat	blood
15	chr4:88044400-88060800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:88044600-88059200	Strong transcription	Primary B cells from peripheral blood	blood
17	chr4:88044600-88060200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:88044600-88061400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr4:88044600-88061600	Strong transcription	Fetal Intestine Large	intestine
20	chr4:88044600-88062200	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr4:88044600-88067600	Strong transcription	Primary B cells from cord blood	blood
22	chr4:88044800-88059400	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr4:88044800-88061400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr4:88044800-88061600	Strong transcription	Duodenum Mucosa	Duodenum
25	chr4:88045000-88060400	Strong transcription	Primary hematopoietic stem cells	blood
26	chr4:88045200-88057800	Strong transcription	HUVEC	blood vessel
27	chr4:88045600-88057600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:88045600-88058800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:88045600-88059200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:88045600-88059600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr4:88045600-88060400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr4:88045600-88063800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:88045600-88063800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:88045800-88054000	Strong transcription	Left Ventricle	heart
35	chr4:88045800-88058200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:88045800-88059200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:88045800-88059800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:88045800-88061200	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr4:88045800-88061400	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr4:88045800-88063000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:88045800-88067600	Strong transcription	Fetal Thymus	thymus
42	chr4:88046000-88054600	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr4:88046000-88058400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:88046000-88058600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:88046000-88059000	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr4:88046000-88059200	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr4:88046000-88059400	Strong transcription	Dnd41	blood
48	chr4:88046000-88061400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr4:88046200-88055200	Strong transcription	NHDF-Ad	bronchial
50	chr4:88046200-88055800	Strong transcription	Brain Inferior Temporal Lobe	brain

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