Variant report

Variant	rs34308676
Chromosome Location	chr2:54774121-54774122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr2:54773660-54774398	K562	blood:	n/a	n/a
2	CHD2	chr2:54774083-54774412	GM12878	blood:	n/a	n/a
3	IRF1	chr2:54773815-54774449	K562	blood:	n/a	n/a
4	MXI1	chr2:54773965-54774302	GM12878	blood:	n/a	n/a
5	ZNF384	chr2:54774119-54774181	GM12878	blood:	n/a	n/a
6	CHD1	chr2:54774111-54774229	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54767808..54771330-chr2:54771769..54776449,4	K562	blood:

Variant related genes	Relation type
ENSG00000234943	TF binding region
ENSG00000228108	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10183043	0.81[EUR][1000 genomes]
rs10210502	0.84[EUR][1000 genomes]
rs10528	0.86[EUR][1000 genomes]
rs11555856	0.89[EUR][1000 genomes]
rs11883910	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11892236	0.85[EUR][1000 genomes]
rs11896957	0.85[EUR][1000 genomes]
rs11904679	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12713262	0.86[EUR][1000 genomes]
rs12713263	0.86[EUR][1000 genomes]
rs12713270	0.82[EUR][1000 genomes]
rs12713271	0.82[EUR][1000 genomes]
rs12713273	0.84[EUR][1000 genomes]
rs12987967	0.90[EUR][1000 genomes]
rs13006815	0.87[EUR][1000 genomes]
rs13021606	0.85[EUR][1000 genomes]
rs13021615	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13036147	0.90[EUR][1000 genomes]
rs13391803	0.90[EUR][1000 genomes]
rs17039558	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17045939	0.90[EUR][1000 genomes]
rs17046061	0.85[EUR][1000 genomes]
rs17046067	0.85[EUR][1000 genomes]
rs17046108	0.81[EUR][1000 genomes]
rs2229503	0.86[EUR][1000 genomes]
rs2271329	0.81[EUR][1000 genomes]
rs34077590	0.92[EUR][1000 genomes]
rs34094680	0.92[EUR][1000 genomes]
rs34263579	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34311770	0.85[EUR][1000 genomes]
rs34429083	0.91[EUR][1000 genomes]
rs34978408	0.92[EUR][1000 genomes]
rs35619551	0.83[EUR][1000 genomes]
rs36018286	0.90[EUR][1000 genomes]
rs3796022	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4261758	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4319969	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4358162	0.82[EUR][1000 genomes]
rs4519566	0.85[EUR][1000 genomes]
rs45487791	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4577321	0.85[EUR][1000 genomes]
rs57281248	0.92[EUR][1000 genomes]
rs58419243	0.85[EUR][1000 genomes]
rs61126015	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545430	0.85[EUR][1000 genomes]
rs6545435	0.83[EUR][1000 genomes]
rs66693131	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67079536	0.86[EUR][1000 genomes]
rs6721612	0.85[EUR][1000 genomes]
rs6724136	0.81[EUR][1000 genomes]
rs67244067	0.80[EUR][1000 genomes]
rs6730876	0.85[EUR][1000 genomes]
rs6734445	0.88[EUR][1000 genomes]
rs6734536	0.92[EUR][1000 genomes]
rs6741053	0.82[EUR][1000 genomes]
rs72806653	0.81[EUR][1000 genomes]
rs7424459	0.88[EUR][1000 genomes]
rs7584223	0.85[EUR][1000 genomes]
rs7586066	0.89[EUR][1000 genomes]
rs7602992	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv528848	chr2:54758305-54777576	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
rs34308676	EML6	cis	Thyroid	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
3	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:54757000-54776800	Weak transcription	Brain Germinal Matrix	brain
5	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
6	chr2:54762000-54775400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:54763000-54776000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:54764000-54776800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:54768200-54783800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:54768400-54775800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:54769800-54775400	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:54769800-54775600	Weak transcription	Fetal Stomach	stomach
13	chr2:54769800-54777000	Weak transcription	Psoas Muscle	Psoas
14	chr2:54770000-54777400	Weak transcription	GM12878-XiMat	blood
15	chr2:54770400-54775000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:54770400-54775400	Weak transcription	Lung	lung
17	chr2:54770400-54776800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:54770400-54782000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:54770600-54775400	Weak transcription	Right Atrium	heart
20	chr2:54770600-54776800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:54770600-54780200	Enhancers	Fetal Intestine Large	intestine
22	chr2:54771600-54783400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:54772400-54774600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:54772600-54774200	Enhancers	Brain Hippocampus Middle	brain
25	chr2:54772600-54774200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr2:54772600-54774200	Enhancers	HMEC	breast
27	chr2:54772600-54774200	Enhancers	NHDF-Ad	bronchial
28	chr2:54772600-54774600	Enhancers	Brain Substantia Nigra	brain
29	chr2:54772600-54778800	Enhancers	Brain Anterior Caudate	brain
30	chr2:54772600-54780200	Enhancers	Fetal Intestine Small	intestine
31	chr2:54772800-54774200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr2:54772800-54774200	Enhancers	Brain Cingulate Gyrus	brain
33	chr2:54772800-54774400	Enhancers	Brain Angular Gyrus	brain
34	chr2:54772800-54774400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:54772800-54774400	Enhancers	K562	blood
36	chr2:54772800-54774600	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr2:54772800-54774600	Enhancers	Fetal Kidney	kidney
38	chr2:54772800-54774800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:54772800-54774800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:54773000-54774800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:54773000-54775400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:54773200-54774400	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr2:54773200-54775400	Weak transcription	Gastric	stomach
44	chr2:54773200-54775400	Weak transcription	Left Ventricle	heart
45	chr2:54773200-54777200	Weak transcription	NHLF	lung
46	chr2:54773400-54774400	Genic enhancers	Fetal Lung	lung
47	chr2:54773400-54774600	Weak transcription	Fetal Brain Male	brain
48	chr2:54773400-54774600	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr2:54773400-54774800	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr2:54773400-54775400	Weak transcription	HSMM	muscle

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