Variant report

Variant	rs9677089
Chromosome Location	chr2:54794927-54794928
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54789909..54791873-chr2:54794483..54796038,2	MCF-7	breast:
2	chr2:54793317..54796723-chr2:54797852..54801262,4	MCF-7	breast:
3	chr2:54772044..54775380-chr2:54793081..54796428,3	K562	blood:

Variant related genes	Relation type
ENSG00000234943	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10166844	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10169954	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10169975	0.84[EUR][1000 genomes]
rs10170066	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10170355	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10182538	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10182836	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10183867	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10184128	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10187338	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10188545	0.84[EUR][1000 genomes]
rs10193692	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10205410	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10206143	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10208225	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10210502	0.83[ASN][1000 genomes]
rs1137645	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11892443	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11898032	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11898033	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11902987	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713264	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12713265	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12713266	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12713267	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713268	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12713269	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13386146	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13391522	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13391803	0.82[ASN][1000 genomes]
rs13399656	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13403284	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13407214	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13423873	0.85[EUR][1000 genomes]
rs13432302	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28581481	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3287	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34077590	0.85[ASN][1000 genomes]
rs3796017	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796018	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4346422	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4347868	0.83[EUR][1000 genomes]
rs4374410	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4455200	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4519566	0.81[ASN][1000 genomes]
rs4577321	0.81[ASN][1000 genomes]
rs4616509	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4641979	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57281248	0.85[ASN][1000 genomes]
rs6706263	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6734445	0.85[ASN][1000 genomes]
rs6734536	0.85[ASN][1000 genomes]
rs6739140	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6749802	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7340302	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7556752	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7564719	0.85[EUR][1000 genomes]
rs7584223	0.81[ASN][1000 genomes]
rs7586066	0.82[ASN][1000 genomes]
rs7586311	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7591231	0.83[EUR][1000 genomes]
rs7599241	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7602992	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9677089	EML6	cis	Thyroid	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54787600-54796800	Weak transcription	Aorta	Aorta
2	chr2:54787600-54797000	Weak transcription	Gastric	stomach
3	chr2:54787800-54796200	Weak transcription	Esophagus	oesophagus
4	chr2:54787800-54797200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:54788000-54796000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:54788200-54795000	Weak transcription	Brain Anterior Caudate	brain
7	chr2:54788400-54797600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:54788600-54795200	Weak transcription	Placenta	Placenta
9	chr2:54788600-54796000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:54788600-54796200	Weak transcription	Colonic Mucosa	Colon
11	chr2:54788600-54796200	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:54788600-54796400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:54788600-54796800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:54788600-54796800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:54788800-54796000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:54789200-54796200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:54789400-54795800	Weak transcription	NHLF	lung
18	chr2:54789400-54796000	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:54789400-54796000	Weak transcription	HSMMtube	muscle
20	chr2:54789400-54796200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:54789400-54796200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:54789400-54796400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:54789600-54795200	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr2:54789600-54795800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:54789600-54795800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:54789600-54795800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:54789600-54795800	Weak transcription	NH-A	brain
28	chr2:54789600-54796000	Weak transcription	Brain Angular Gyrus	brain
29	chr2:54789600-54796000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr2:54789600-54796000	Weak transcription	Brain Substantia Nigra	brain
31	chr2:54789600-54796000	Weak transcription	HMEC	breast
32	chr2:54789600-54796000	Weak transcription	HSMM	muscle
33	chr2:54789600-54796000	Weak transcription	NHDF-Ad	bronchial
34	chr2:54789600-54796000	Weak transcription	Osteobl	bone
35	chr2:54789600-54796200	Enhancers	Primary B cells from peripheral blood	blood
36	chr2:54789600-54796800	Weak transcription	Psoas Muscle	Psoas
37	chr2:54789800-54795000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:54789800-54795200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr2:54789800-54795800	Weak transcription	NHEK	skin
40	chr2:54789800-54796000	Enhancers	Primary T cells fromperipheralblood	blood
41	chr2:54789800-54801400	Enhancers	Liver	Liver
42	chr2:54790000-54795800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:54790000-54796000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr2:54790000-54796200	Weak transcription	Fetal Brain Male	brain
45	chr2:54790000-54797200	Weak transcription	Lung	lung
46	chr2:54790200-54795600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:54790200-54796000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:54790200-54796000	Weak transcription	Thymus	Thymus
49	chr2:54790400-54795800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:54790400-54796400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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