Variant report

Variant	rs42088
Chromosome Location	chr7:27701861-27701862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:27699948..27706867-chr7:27775418..27784557,21	K562	blood:
2	chr7:27236687..27240147-chr7:27700482..27703881,4	MCF-7	breast:
3	chr7:27700432..27708426-chr7:27777901..27782637,20	K562	blood:
4	chr7:27683238..27686039-chr7:27700325..27702325,3	K562	blood:

Variant related genes	Relation type
ENSG00000106031	Chromatin interaction
ENSG00000243766	Chromatin interaction
ENSG00000106052	Chromatin interaction
ENSG00000229893	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10081338	0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10081339	0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1014373	0.88[YRI][hapmap]
rs1015265	0.89[YRI][hapmap]
rs10447552	0.92[LWK][hapmap]
rs10486548	0.97[GIH][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10951173	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11764753	0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs12531518	0.89[AFR][1000 genomes]
rs12537499	0.83[LWK][hapmap]
rs12540063	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12668430	0.83[LWK][hapmap]
rs12673949	0.88[YRI][hapmap]
rs12700823	0.89[AFR][1000 genomes]
rs12700824	0.82[ASN][1000 genomes]
rs12700825	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12700829	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12700830	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1404276	0.89[YRI][hapmap]
rs1404282	0.97[GIH][hapmap];0.80[MEX][hapmap];0.89[YRI][hapmap]
rs1524529	0.89[YRI][hapmap]
rs1608663	0.97[GIH][hapmap];0.80[MEX][hapmap];0.89[YRI][hapmap]
rs1880370	0.88[YRI][hapmap]
rs1980330	0.89[YRI][hapmap]
rs2041714	0.83[LWK][hapmap]
rs2160125	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2391444	0.89[YRI][hapmap]
rs2391445	1.00[YRI][hapmap]
rs2391446	1.00[YRI][hapmap]
rs2391447	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2391448	0.82[ASN][1000 genomes]
rs2391451	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2391454	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs42085	0.92[LWK][hapmap]
rs42087	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs42098	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4719902	0.89[YRI][hapmap]
rs4722726	1.00[CHB][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs4722728	0.92[LWK][hapmap]
rs6462033	0.89[YRI][hapmap]
rs6462039	0.94[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6943883	0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs6946305	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6954905	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6957378	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6958747	0.90[LWK][hapmap]
rs6966091	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6974932	0.92[LWK][hapmap]
rs7779990	1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs7782422	0.87[AFR][1000 genomes]
rs7786973	0.86[YRI][hapmap]
rs7806415	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7808275	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs961723	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs961724	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs961725	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs9639552	1.00[YRI][hapmap]
rs974883	0.88[YRI][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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs42088	HIBADH	cis	lymphoblastoid	seeQTL
rs42088	HIBADH	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27700600-27703600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr7:27700800-27703400	Active TSS	NHLF	lung
3	chr7:27701000-27703200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:27701000-27703400	Active TSS	A549	lung
5	chr7:27701000-27703400	Active TSS	HSMM	muscle
6	chr7:27701000-27703400	Active TSS	K562	blood
7	chr7:27701200-27702000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr7:27701200-27702600	Active TSS	Small Intestine	intestine
9	chr7:27701200-27703000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:27701200-27703000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:27701200-27703200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr7:27701200-27703200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr7:27701200-27703400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:27701200-27703400	Active TSS	Muscle Satellite Cultured Cells	--
15	chr7:27701200-27703400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:27701200-27703600	Active TSS	NHDF-Ad	bronchial
17	chr7:27701400-27702000	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr7:27701400-27702000	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr7:27701400-27702000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr7:27701400-27702000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr7:27701400-27702000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr7:27701400-27702000	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr7:27701400-27702000	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr7:27701400-27702000	Flanking Active TSS	Fetal Muscle Leg	muscle
25	chr7:27701400-27702000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr7:27701400-27702000	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr7:27701400-27702000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr7:27701400-27702000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr7:27701400-27702000	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr7:27701400-27702000	Flanking Active TSS	Thymus	Thymus
31	chr7:27701400-27702000	Flanking Active TSS	HUVEC	blood vessel
32	chr7:27701400-27702000	Flanking Active TSS	NH-A	brain
33	chr7:27701400-27702000	Flanking Active TSS	NHEK	skin
34	chr7:27701400-27702200	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr7:27701400-27702200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr7:27701400-27702200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr7:27701400-27702200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr7:27701400-27702200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr7:27701400-27702600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:27701400-27702800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr7:27701400-27703000	Active TSS	H1 Cell Line	embryonic stem cell
42	chr7:27701400-27703000	Active TSS	H9 Cell Line	embryonic stem cell
43	chr7:27701400-27703000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr7:27701400-27703200	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr7:27701400-27703200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr7:27701400-27703200	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr7:27701400-27703200	Active TSS	Brain Substantia Nigra	brain
48	chr7:27701400-27703200	Active TSS	Fetal Muscle Trunk	muscle
49	chr7:27701400-27703200	Active TSS	Placenta	Placenta
50	chr7:27701400-27703200	Active TSS	Pancreas	Pancrea

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