Variant report

Variant	rs12987967
Chromosome Location	chr2:54785705-54785706
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54785416..54786973-chr2:54949128..54950959,2	K562	blood:
2	chr2:54341806..54344770-chr2:54784235..54787039,2	MCF-7	breast:
3	chr2:54764431..54771229-chr2:54784220..54787609,7	MCF-7	breast:
4	chr2:54754602..54758699-chr2:54783105..54787010,4	MCF-7	breast:
5	chr2:54749132..54757147-chr2:54784492..54789269,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction
ENSG00000237887	Chromatin interaction
ENSG00000214595	Chromatin interaction
ENSG00000228108	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10166844	0.84[ASN][1000 genomes]
rs10170066	0.81[ASN][1000 genomes]
rs10170355	0.81[ASN][1000 genomes]
rs10176359	0.80[EUR][1000 genomes]
rs10182538	0.81[ASN][1000 genomes]
rs10182836	0.81[ASN][1000 genomes]
rs10183043	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10183867	0.81[ASN][1000 genomes]
rs10184128	0.82[ASN][1000 genomes]
rs10187338	0.81[ASN][1000 genomes]
rs10188545	0.83[ASN][1000 genomes]
rs10193692	0.81[ASN][1000 genomes]
rs10205410	0.82[ASN][1000 genomes]
rs10206143	0.81[ASN][1000 genomes]
rs10208225	0.81[ASN][1000 genomes]
rs10210502	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10528	0.87[EUR][1000 genomes]
rs1137645	0.81[ASN][1000 genomes]
rs11555856	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11892236	0.85[EUR][1000 genomes]
rs11892443	0.81[ASN][1000 genomes]
rs11896957	0.88[EUR][1000 genomes]
rs11898032	0.84[ASN][1000 genomes]
rs11898033	0.84[ASN][1000 genomes]
rs11902659	0.80[EUR][1000 genomes]
rs11904679	0.86[EUR][1000 genomes]
rs12713262	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713263	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713264	0.81[ASN][1000 genomes]
rs12713265	0.81[ASN][1000 genomes]
rs12713266	0.81[ASN][1000 genomes]
rs12713268	0.81[ASN][1000 genomes]
rs12713269	0.81[ASN][1000 genomes]
rs12713270	0.84[EUR][1000 genomes]
rs12713271	0.84[EUR][1000 genomes]
rs12713272	0.80[EUR][1000 genomes]
rs12713273	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713274	0.81[ASN][1000 genomes]
rs13004944	0.82[EUR][1000 genomes]
rs13021606	0.88[EUR][1000 genomes]
rs13021615	0.87[EUR][1000 genomes]
rs13036147	0.81[EUR][1000 genomes]
rs13386146	0.82[ASN][1000 genomes]
rs13391522	0.81[ASN][1000 genomes]
rs13391803	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13399656	0.82[ASN][1000 genomes]
rs13403284	0.81[ASN][1000 genomes]
rs13407214	0.82[ASN][1000 genomes]
rs13423873	0.91[ASN][1000 genomes]
rs13432302	0.81[ASN][1000 genomes]
rs17039558	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17045939	0.81[EUR][1000 genomes]
rs17046036	0.82[EUR][1000 genomes]
rs17046061	0.85[EUR][1000 genomes]
rs17046067	0.85[EUR][1000 genomes]
rs17046108	0.81[EUR][1000 genomes]
rs2229503	0.87[EUR][1000 genomes]
rs3287	0.81[ASN][1000 genomes]
rs34077590	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34094680	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34263579	0.85[EUR][1000 genomes]
rs34308676	0.90[EUR][1000 genomes]
rs34311770	0.85[EUR][1000 genomes]
rs34429083	0.82[EUR][1000 genomes]
rs34978408	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35619551	0.84[EUR][1000 genomes]
rs36018286	0.81[EUR][1000 genomes]
rs3796017	0.81[ASN][1000 genomes]
rs3796018	0.81[ASN][1000 genomes]
rs3796022	0.87[EUR][1000 genomes]
rs4261758	0.88[EUR][1000 genomes]
rs4319969	0.84[EUR][1000 genomes]
rs4346422	0.82[ASN][1000 genomes]
rs4347868	0.84[ASN][1000 genomes]
rs4358162	0.84[EUR][1000 genomes]
rs4374410	0.86[ASN][1000 genomes]
rs4455200	0.82[ASN][1000 genomes]
rs4519566	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs45487791	0.83[EUR][1000 genomes]
rs4577321	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4616509	0.81[ASN][1000 genomes]
rs4641979	0.81[ASN][1000 genomes]
rs57281248	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58419243	0.85[EUR][1000 genomes]
rs61126015	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545430	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545435	0.83[EUR][1000 genomes]
rs66693131	0.87[EUR][1000 genomes]
rs6706263	0.81[ASN][1000 genomes]
rs67079536	0.89[EUR][1000 genomes]
rs6721612	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6724136	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67244067	0.82[EUR][1000 genomes]
rs6730876	0.88[EUR][1000 genomes]
rs6734445	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6734536	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6739140	0.84[ASN][1000 genomes]
rs6741053	0.84[EUR][1000 genomes]
rs6749802	0.84[ASN][1000 genomes]
rs72806653	0.81[EUR][1000 genomes]
rs7340302	0.82[ASN][1000 genomes]
rs7424459	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7556752	0.81[ASN][1000 genomes]
rs7564719	0.83[ASN][1000 genomes]
rs7569127	0.80[EUR][1000 genomes]
rs7584223	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7586066	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7586311	0.81[ASN][1000 genomes]
rs7599241	0.82[ASN][1000 genomes]
rs7602992	0.89[EUR][1000 genomes];0.87[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	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	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
rs12987967	EML6	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54784000-54788200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr2:54784200-54786200	Enhancers	Fetal Brain Male	brain
3	chr2:54784200-54788400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr2:54784400-54788400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:54784600-54785800	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr2:54784600-54785800	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr2:54784600-54785800	Active TSS	Rectal Smooth Muscle	rectum
8	chr2:54784600-54787800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:54784600-54787800	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr2:54784600-54787800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:54784600-54787800	Flanking Active TSS	Fetal Muscle Leg	muscle
12	chr2:54784600-54788000	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr2:54784600-54788200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:54784600-54788200	Active TSS	Sigmoid Colon	Sigmoid Colon
15	chr2:54784600-54788400	Active TSS	Thymus	Thymus
16	chr2:54784600-54788600	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr2:54784600-54788800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:54784800-54785800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:54784800-54785800	Active TSS	Brain Anterior Caudate	brain
20	chr2:54784800-54785800	Active TSS	Colon Smooth Muscle	Colon
21	chr2:54784800-54785800	Active TSS	Placenta	Placenta
22	chr2:54784800-54785800	Active TSS	Ovary	ovary
23	chr2:54784800-54786000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr2:54784800-54786000	Flanking Active TSS	Fetal Muscle Trunk	muscle
25	chr2:54784800-54786000	Active TSS	A549	lung
26	chr2:54784800-54786200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:54784800-54786200	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr2:54784800-54786400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:54784800-54786400	Active TSS	Aorta	Aorta
30	chr2:54784800-54786400	Flanking Active TSS	Left Ventricle	heart
31	chr2:54784800-54786600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr2:54784800-54786800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:54784800-54787000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:54784800-54787000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:54784800-54787600	Active TSS	Gastric	stomach
36	chr2:54784800-54787800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:54784800-54787800	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr2:54784800-54787800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:54784800-54787800	Active TSS	Esophagus	oesophagus
40	chr2:54784800-54788000	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr2:54784800-54788000	Active TSS	Liver	Liver
42	chr2:54784800-54788200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:54784800-54788200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:54784800-54788200	Active TSS	Lung	lung
45	chr2:54784800-54788400	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr2:54784800-54788400	Active TSS	Fetal Intestine Small	intestine
47	chr2:54784800-54788400	Active TSS	Pancreas	Pancrea
48	chr2:54784800-54788600	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr2:54784800-54789000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:54784800-54789800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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