Variant report

Variant	rs4073054
Chromosome Location	chr1:161200487-161200488
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161198933..161201204-chr1:161201944..161204407,2	MCF-7	breast:
2	chr1:161187330..161192033-chr1:161197583..161201870,4	K562	blood:
3	chr1:161199382..161202351-chr1:161336794..161339245,2	K562	blood:
4	chr1:161194292..161205045-chr1:161279588..161288493,17	K562	blood:

Variant related genes	Relation type
ENSG00000268387	Chromatin interaction
ENSG00000235477	Chromatin interaction
ENSG00000158887	Chromatin interaction
ENSG00000188931	Chromatin interaction
ENSG00000143257	Chromatin interaction
ENSG00000143252	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10797094	0.87[GIH][hapmap]
rs2502802	0.81[YRI][hapmap]
rs4233367	0.82[GIH][hapmap]
rs4589131	0.87[GIH][hapmap]
rs4656292	0.88[EUR][1000 genomes]
rs4656993	0.87[GIH][hapmap]
rs5082	0.84[ASW][hapmap];0.96[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7512012	0.82[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Blood metabolite levels	24816252	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4073054	TOMM40L	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161196400-161207800	Weak transcription	Small Intestine	intestine
2	chr1:161197600-161200600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:161197600-161200800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:161197600-161201200	Genic enhancers	Fetal Intestine Small	intestine
5	chr1:161197600-161202200	Weak transcription	Fetal Brain Male	brain
6	chr1:161197600-161202600	Weak transcription	Fetal Kidney	kidney
7	chr1:161197600-161203200	Weak transcription	Right Atrium	heart
8	chr1:161197600-161205600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:161197800-161200600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:161197800-161200600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:161197800-161200600	Strong transcription	Brain Cingulate Gyrus	brain
12	chr1:161197800-161200600	Strong transcription	Brain Inferior Temporal Lobe	brain
13	chr1:161197800-161200800	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr1:161197800-161200800	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:161197800-161201000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:161197800-161201200	Strong transcription	Left Ventricle	heart
17	chr1:161197800-161201400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:161197800-161201800	Strong transcription	Fetal Brain Female	brain
19	chr1:161197800-161202400	Weak transcription	Stomach Mucosa	stomach
20	chr1:161198000-161200600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:161198000-161200600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:161198000-161200600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:161198000-161200600	Strong transcription	Adipose Nuclei	Adipose
24	chr1:161198000-161200600	Strong transcription	Brain Substantia Nigra	brain
25	chr1:161198000-161200600	Strong transcription	Dnd41	blood
26	chr1:161198000-161200600	Strong transcription	K562	blood
27	chr1:161198000-161200800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:161198000-161200800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:161198000-161200800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:161198000-161200800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:161198000-161200800	Strong transcription	Brain Anterior Caudate	brain
32	chr1:161198000-161200800	Strong transcription	Brain Hippocampus Middle	brain
33	chr1:161198000-161200800	Strong transcription	Esophagus	oesophagus
34	chr1:161198000-161200800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:161198000-161200800	Strong transcription	Fetal Muscle Trunk	muscle
36	chr1:161198000-161200800	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:161198000-161200800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:161198000-161200800	Strong transcription	Right Ventricle	heart
39	chr1:161198000-161200800	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:161198000-161200800	Strong transcription	Stomach Smooth Muscle	stomach
41	chr1:161198000-161201000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:161198000-161201000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:161198000-161201000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:161198000-161201000	Strong transcription	Thymus	Thymus
45	chr1:161198000-161201200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:161198000-161201200	Strong transcription	Brain Germinal Matrix	brain
47	chr1:161198000-161201200	Strong transcription	Placenta	Placenta
48	chr1:161198000-161201200	Strong transcription	Lung	lung
49	chr1:161198000-161201200	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:161198000-161201800	Weak transcription	Psoas Muscle	Psoas

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