Variant report

Variant	rs11898032
Chromosome Location	chr2:54821515-54821516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54782515..54784267-chr2:54820223..54822640,2	MCF-7	breast:
2	chr2:54785168..54787003-chr2:54819314..54822161,2	K562	blood:
3	chr2:54815707..54819448-chr2:54820160..54824681,7	K562	blood:
4	chr2:54815000..54820095-chr2:54820709..54825309,10	K562	blood:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10166844	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10169954	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10169975	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10170066	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10170355	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10176445	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10182538	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10182836	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10183043	0.95[ASN][1000 genomes]
rs10183867	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10184128	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10187338	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10188545	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10193692	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10205410	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10206143	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10208225	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10210502	0.94[ASN][1000 genomes]
rs1137645	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11892443	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11896957	0.82[ASN][1000 genomes]
rs11898033	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902987	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12713262	0.83[ASN][1000 genomes]
rs12713263	0.83[ASN][1000 genomes]
rs12713264	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713265	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713266	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713267	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12713268	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713269	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713270	0.82[ASN][1000 genomes]
rs12713271	0.82[ASN][1000 genomes]
rs12713273	0.92[ASN][1000 genomes]
rs12713274	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12987967	0.84[ASN][1000 genomes]
rs13386146	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13391522	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13391803	0.92[ASN][1000 genomes]
rs13399656	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13403284	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13407214	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13423873	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13432302	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17046097	0.88[EUR][1000 genomes]
rs28581481	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3287	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34077590	0.89[ASN][1000 genomes]
rs34094680	0.89[ASN][1000 genomes]
rs34978408	0.83[ASN][1000 genomes]
rs3796017	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796018	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4346422	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4347868	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4358162	0.82[ASN][1000 genomes]
rs4374410	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4455200	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4519566	0.97[ASN][1000 genomes]
rs4577321	0.97[ASN][1000 genomes]
rs4616509	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4641979	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57281248	0.89[ASN][1000 genomes]
rs6545430	0.86[ASN][1000 genomes]
rs6706263	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6721612	0.82[ASN][1000 genomes]
rs6724136	0.86[ASN][1000 genomes]
rs6730876	0.82[ASN][1000 genomes]
rs6734445	0.92[ASN][1000 genomes]
rs6734536	0.89[ASN][1000 genomes]
rs6739140	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740893	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6749802	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7340302	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7424459	0.95[ASN][1000 genomes]
rs7556752	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7564719	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7584223	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7586066	0.92[ASN][1000 genomes]
rs7586311	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7591204	0.91[EUR][1000 genomes]
rs7591231	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7599241	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7602992	0.90[ASN][1000 genomes]
rs7608414	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9677089	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	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
3	nsv961318	chr2:54818096-54823449	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11898032	EML6	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54802200-54822600	Weak transcription	Esophagus	oesophagus
2	chr2:54804000-54822400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:54805400-54830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:54807000-54826000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:54808800-54822800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:54809400-54821600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr2:54809600-54825800	Weak transcription	Brain Germinal Matrix	brain
8	chr2:54814000-54822800	Weak transcription	Ovary	ovary
9	chr2:54815400-54823400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:54816200-54830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:54816600-54822400	Weak transcription	Gastric	stomach
12	chr2:54816600-54822400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:54816600-54822600	Weak transcription	Colonic Mucosa	Colon
14	chr2:54816600-54828400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:54816800-54822400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:54816800-54822600	Weak transcription	Placenta	Placenta
17	chr2:54816800-54823000	Weak transcription	Aorta	Aorta
18	chr2:54816800-54823200	Weak transcription	Fetal Kidney	kidney
19	chr2:54816800-54823400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:54817000-54822400	Weak transcription	NHLF	lung
21	chr2:54817000-54822600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:54817000-54822800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:54817000-54823200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:54817000-54823200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:54817000-54825800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:54817000-54826200	Weak transcription	NHDF-Ad	bronchial
27	chr2:54817400-54822600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:54817400-54823000	Weak transcription	Dnd41	blood
29	chr2:54817400-54823200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr2:54817400-54823400	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr2:54817400-54825400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:54817600-54822400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:54817600-54822600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:54817600-54822800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:54817600-54823600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:54817600-54825000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:54817600-54825600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:54817800-54822200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:54817800-54822400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr2:54817800-54822600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:54817800-54822800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:54817800-54823000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr2:54817800-54823000	Weak transcription	NH-A	brain
44	chr2:54817800-54823400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:54817800-54825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:54817800-54826200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr2:54817800-54826200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr2:54818000-54822200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:54818000-54822400	Weak transcription	Right Ventricle	heart
50	chr2:54818000-54824400	Weak transcription	HMEC	breast

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