Variant report

Variant	rs2438146
Chromosome Location	chr4:95395388-95395389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95388967..95390908-chr4:95394700..95396781,2	K562	blood:
2	chr4:95370572..95375006-chr4:95392814..95398677,7	K562	blood:
3	chr4:95394803..95397369-chr4:95447268..95448827,2	K562	blood:
4	chr4:95391486..95396177-chr4:95398178..95402962,4	K562	blood:

Variant related genes	Relation type
ENSG00000203436	Chromatin interaction
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs17378777	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1820475	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2011525	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2433320	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2433322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2433323	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2433326	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2433327	0.88[CEU][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]
rs2438140	0.86[MEX][hapmap]
rs2438147	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2438148	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2452553	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2510762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2510763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2510765	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2510800	0.81[JPT][hapmap]
rs2639793	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs28697067	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34570027	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3805301	0.83[YRI][hapmap]
rs6812165	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs774982	0.88[CEU][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs774984	0.86[MEX][hapmap]
rs9990678	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9990976	0.81[CEU][hapmap];0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv594901	chr4:95254730-95493246	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1003743	chr4:95255957-95469831	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95374200-95395400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:95374200-95400000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:95374800-95398200	Weak transcription	Esophagus	oesophagus
4	chr4:95375000-95440200	Weak transcription	Primary T cells from cord blood	blood
5	chr4:95375800-95401600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:95379200-95398400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr4:95383000-95395800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr4:95383000-95396000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr4:95383000-95396000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:95387400-95410000	Weak transcription	NHLF	lung
11	chr4:95387400-95420800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:95389600-95406000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:95390800-95395800	Weak transcription	Ovary	ovary
14	chr4:95390800-95397000	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:95390800-95397800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:95390800-95398200	Weak transcription	Gastric	stomach
17	chr4:95392200-95395800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:95392400-95395800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:95392600-95399200	Enhancers	Liver	Liver
20	chr4:95392800-95398000	Enhancers	HepG2	liver
21	chr4:95393600-95395400	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr4:95393800-95397800	Weak transcription	NHEK	skin
23	chr4:95393800-95398000	Weak transcription	HMEC	breast
24	chr4:95393800-95398200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:95393800-95398400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:95393800-95399200	Enhancers	Fetal Heart	heart
27	chr4:95393800-95401600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:95393800-95405600	Weak transcription	HSMMtube	muscle
29	chr4:95394000-95396400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:95394000-95397800	Weak transcription	Right Ventricle	heart
31	chr4:95394000-95397800	Weak transcription	Small Intestine	intestine
32	chr4:95394000-95398200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:95394000-95398400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:95394000-95405000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:95394200-95395400	Strong transcription	HSMM	muscle
36	chr4:95394200-95401400	Weak transcription	Brain Anterior Caudate	brain
37	chr4:95394200-95404800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:95394400-95395400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:95394400-95396000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr4:95394400-95396400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:95394400-95398000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr4:95394400-95398000	Weak transcription	Hela-S3	cervix
43	chr4:95394400-95398200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:95394400-95400600	Weak transcription	Adipose Nuclei	Adipose
45	chr4:95394400-95405800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:95394400-95407000	Weak transcription	NH-A	brain
47	chr4:95394400-95407800	Weak transcription	Aorta	Aorta
48	chr4:95394400-95419200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr4:95394400-95428000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr4:95394600-95395600	Weak transcription	Psoas Muscle	Psoas

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