Variant report

Variant	rs342435
Chromosome Location	chr4:88043206-88043207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:88041232..88043598-chr4:88048942..88050485,2	MCF-7	breast:
2	chr4:88042372..88045349-chr4:88046693..88048270,2	K562	blood:
3	chr4:87926518..87929416-chr4:88041229..88043672,2	K562	blood:
4	chr4:88037805..88040790-chr4:88041752..88044910,3	MCF-7	breast:
5	chr4:88042535..88044743-chr4:88048673..88050393,2	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10023050	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1037814	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11097127	0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1408	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1674999	0.94[ASN][1000 genomes]
rs16930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17012368	0.90[ASN][1000 genomes]
rs2045592	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2125787	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs236984	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs236985	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs236987	0.94[ASN][1000 genomes]
rs236992	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs236993	0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs236995	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs236996	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs2926511	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs342437	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs342438	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs342452	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs342453	0.94[ASN][1000 genomes]
rs342454	0.94[ASN][1000 genomes]
rs342456	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs342466	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs342467	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs342468	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs342469	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs3736669	0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs3775214	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs3775217	0.93[ASN][1000 genomes]
rs3775220	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs3775221	0.93[ASN][1000 genomes]
rs3775223	0.93[ASN][1000 genomes]
rs442177	0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs4693156	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs7660883	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs9998251	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:127 , 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	chr4:88030000-88048800	Weak transcription	A549	lung
5	chr4:88030600-88057600	Weak transcription	Brain Germinal Matrix	brain
6	chr4:88032800-88043600	Strong transcription	Fetal Thymus	thymus
7	chr4:88032800-88059000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr4:88033600-88047600	Weak transcription	HSMM	muscle
9	chr4:88034800-88043400	Weak transcription	Hela-S3	cervix
10	chr4:88035600-88056800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:88035600-88063800	Strong transcription	Primary T cells from cord blood	blood
12	chr4:88036400-88063600	Weak transcription	Fetal Brain Male	brain
13	chr4:88036800-88046600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:88036800-88046800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:88036800-88059200	Weak transcription	Fetal Brain Female	brain
16	chr4:88038000-88046200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:88038000-88046200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr4:88038400-88046600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr4:88038600-88045800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:88038800-88046000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:88038800-88046800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:88038800-88047000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr4:88039600-88045800	Weak transcription	K562	blood
24	chr4:88039600-88046800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr4:88039800-88043800	Enhancers	Psoas Muscle	Psoas
26	chr4:88040000-88047200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr4:88040000-88052000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:88040200-88043600	Genic enhancers	GM12878-XiMat	blood
29	chr4:88040400-88043800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:88040400-88043800	Strong transcription	Dnd41	blood
31	chr4:88040600-88043800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr4:88040600-88045800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:88040800-88043800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:88040800-88045600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:88040800-88046200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr4:88041000-88043800	Flanking Active TSS	HMEC	breast
37	chr4:88041000-88043800	Flanking Active TSS	NHEK	skin
38	chr4:88041200-88043600	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr4:88041200-88043600	Enhancers	Osteobl	bone
40	chr4:88041200-88043800	Enhancers	Fetal Kidney	kidney
41	chr4:88041200-88043800	Enhancers	HSMMtube	muscle
42	chr4:88041200-88048800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr4:88041400-88043400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:88041400-88043800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr4:88041400-88043800	Enhancers	Brain Angular Gyrus	brain
46	chr4:88041400-88043800	Enhancers	Fetal Muscle Leg	muscle
47	chr4:88041600-88045000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:88041800-88043400	Enhancers	Stomach Mucosa	stomach
49	chr4:88041800-88043800	Enhancers	Muscle Satellite Cultured Cells	--
50	chr4:88041800-88045600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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