Variant report

Variant	rs342459
Chromosome Location	chr4:88059415-88059416
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	chr4:88052295..88056117-chr4:88057226..88059764,4	K562	blood:
2	chr4:88057518..88060731-chr4:88068893..88070799,3	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10018897	0.86[ASN][1000 genomes]
rs1037814	0.82[LWK][hapmap]
rs10516789	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs168204	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs19026	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs236674	0.94[ASN][1000 genomes]
rs236675	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs236678	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs236685	0.94[ASN][1000 genomes]
rs236686	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs236687	0.94[ASN][1000 genomes]
rs2869642	0.92[ASN][1000 genomes]
rs2926512	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3116679	0.94[ASN][1000 genomes]
rs342436	0.87[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs342457	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs342458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342460	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs342461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[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]
rs342462	0.80[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs342465	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs342467	0.81[LWK][hapmap]
rs3775225	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3822042	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs384059	0.87[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs390604	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs393991	0.86[ASN][1000 genomes]
rs411365	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs447990	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60757751	0.96[ASN][1000 genomes]
rs6827213	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9992235	0.86[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	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
8	nsv964300	chr4:88058711-88061227	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs342459	TIGD2	cis	cerebellum	SCAN
rs342459	HSD17B13	cis	cerebellum	SCAN
rs342459	HSD17B13	cis	parietal	SCAN

Chromatin state (count:121 , 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	chr4:88035600-88063800	Strong transcription	Primary T cells from cord blood	blood
4	chr4:88036400-88063600	Weak transcription	Fetal Brain Male	brain
5	chr4:88042800-88069400	Strong transcription	Placenta	Placenta
6	chr4:88043000-88061400	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr4:88043400-88064800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:88043600-88064600	Strong transcription	GM12878-XiMat	blood
9	chr4:88044400-88060800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:88044600-88060200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr4:88044600-88061400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr4:88044600-88061600	Strong transcription	Fetal Intestine Large	intestine
13	chr4:88044600-88062200	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr4:88044600-88067600	Strong transcription	Primary B cells from cord blood	blood
15	chr4:88044800-88061400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr4:88044800-88061600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr4:88045000-88060400	Strong transcription	Primary hematopoietic stem cells	blood
18	chr4:88045600-88059600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:88045600-88060400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:88045600-88063800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:88045600-88063800	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:88045800-88059800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr4:88045800-88061200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:88045800-88061400	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:88045800-88063000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:88045800-88067600	Strong transcription	Fetal Thymus	thymus
27	chr4:88046000-88061400	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr4:88046200-88059800	Strong transcription	Fetal Lung	lung
29	chr4:88046200-88061200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr4:88046200-88061400	Strong transcription	Adipose Nuclei	Adipose
31	chr4:88046200-88061400	Strong transcription	Stomach Smooth Muscle	stomach
32	chr4:88046200-88064200	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr4:88047200-88067000	Strong transcription	Liver	Liver
34	chr4:88047800-88064200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:88049400-88059800	Strong transcription	HepG2	liver
36	chr4:88049400-88064200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:88051800-88060200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr4:88053600-88082000	Weak transcription	HSMM	muscle
39	chr4:88054400-88066800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:88055000-88061400	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr4:88055200-88061000	Weak transcription	NHDF-Ad	bronchial
42	chr4:88055200-88102800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr4:88055400-88072200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr4:88055600-88061400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr4:88055600-88065400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr4:88055600-88072200	Weak transcription	Fetal Kidney	kidney
47	chr4:88055800-88062200	Weak transcription	K562	blood
48	chr4:88055800-88068200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:88056200-88061600	Strong transcription	Left Ventricle	heart
50	chr4:88056200-88062400	Weak transcription	NHLF	lung

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