Variant report

Variant	rs9789534
Chromosome Location	chr2:74362990-74362991
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74345218..74347575-chr2:74362895..74365930,3	MCF-7	breast:
2	chr2:74359306..74360989-chr2:74362559..74364290,2	MCF-7	breast:
3	chr2:74361954..74364751-chr2:74477805..74479595,2	MCF-7	breast:
4	chr2:74356708..74358883-chr2:74362646..74364530,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188687	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs6546891	0.86[JPT][hapmap]
rs7570950	0.86[JPT][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	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
3	nsv525117	chr2:74358901-74374641	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9789534	MGC10955	cis	Skin Sun Exposed Lower leg	GTEx
rs9789534	MGC10955	cis	Artery Tibial	GTEx
rs9789534	NAT8	cis	parietal	SCAN
rs9789534	MGC10955	cis	Esophagus Mucosa	GTEx
rs9789534	MGC10955	cis	Esophagus Muscularis	GTEx
rs9789534	MGC10955	cis	Nerve Tibial	GTEx
rs9789534	MGC10955	cis	Adipose Subcutaneous	GTEx
rs9789534	MGC10955	cis	lung	GTEx
rs9789534	MGC10955	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74348200-74367600	Weak transcription	Brain Anterior Caudate	brain
2	chr2:74354400-74373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:74355200-74373800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:74357600-74373800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:74357800-74367600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:74357800-74373600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:74358200-74364800	Weak transcription	Esophagus	oesophagus
8	chr2:74358200-74373800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:74358600-74367800	Weak transcription	Osteobl	bone
10	chr2:74358600-74368800	Weak transcription	NHDF-Ad	bronchial
11	chr2:74358800-74373800	Weak transcription	HUVEC	blood vessel
12	chr2:74359200-74373600	Weak transcription	Fetal Heart	heart
13	chr2:74359400-74367600	Weak transcription	HSMM	muscle
14	chr2:74359400-74373600	Weak transcription	Primary B cells from cord blood	blood
15	chr2:74359600-74373400	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:74359600-74373800	Weak transcription	Small Intestine	intestine
17	chr2:74359800-74373600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:74359800-74373600	Weak transcription	NH-A	brain
19	chr2:74360000-74369800	Weak transcription	Colonic Mucosa	Colon
20	chr2:74360200-74373600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:74360400-74363000	Strong transcription	Fetal Brain Female	brain
22	chr2:74360400-74363400	Strong transcription	Fetal Stomach	stomach
23	chr2:74360400-74363400	Strong transcription	Dnd41	blood
24	chr2:74360400-74366600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:74360600-74363000	Strong transcription	HepG2	liver
26	chr2:74360600-74373600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:74360800-74373600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr2:74360800-74373800	Weak transcription	Placenta	Placenta
29	chr2:74360800-74374000	Weak transcription	HSMMtube	muscle
30	chr2:74361200-74363000	Strong transcription	Fetal Thymus	thymus
31	chr2:74361200-74365800	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:74361400-74363000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:74361800-74363200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:74362000-74371600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr2:74362000-74373600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:74362200-74363600	Weak transcription	K562	blood
37	chr2:74362200-74363800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:74362200-74365000	Weak transcription	Ovary	ovary
39	chr2:74362200-74365200	Weak transcription	A549	lung
40	chr2:74362200-74365400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:74362200-74365400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:74362200-74366000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:74362200-74366400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:74362200-74366400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:74362200-74366400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr2:74362200-74366600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:74362200-74366800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:74362200-74367600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:74362200-74367600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:74362200-74367600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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