Variant report

Variant	rs6724136
Chromosome Location	chr2:54837377-54837378
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54837203..54842761-chr2:54843020..54847377,6	K562	blood:
2	chr2:54829846..54832829-chr2:54836570..54839601,3	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10166844	0.83[ASN][1000 genomes]
rs10169439	0.90[CEU][hapmap]
rs10169954	0.82[ASN][1000 genomes]
rs10170066	0.83[ASN][1000 genomes]
rs10170355	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10176359	0.86[CEU][hapmap];0.88[CHB][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10176445	0.88[CHB][hapmap]
rs10182538	0.83[ASN][1000 genomes]
rs10182836	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10183043	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10183867	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10184128	0.88[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs10187338	0.83[ASN][1000 genomes]
rs10188185	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs10188545	0.85[ASN][1000 genomes]
rs10193692	0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10193877	0.82[EUR][1000 genomes]
rs10205410	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs10206143	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10208225	0.83[ASN][1000 genomes]
rs10210502	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10528	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1137645	0.88[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs11555856	0.80[EUR][1000 genomes]
rs11892236	0.91[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs11892443	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11896957	0.84[EUR][1000 genomes]
rs11898032	0.86[ASN][1000 genomes]
rs11898033	0.86[ASN][1000 genomes]
rs11902659	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11902987	0.88[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs12713262	0.86[EUR][1000 genomes]
rs12713263	0.86[EUR][1000 genomes]
rs12713264	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs12713265	0.88[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs12713266	0.83[ASN][1000 genomes]
rs12713267	0.80[ASN][1000 genomes]
rs12713268	0.88[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs12713269	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12713270	0.87[EUR][1000 genomes]
rs12713271	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12713272	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12713273	0.93[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12713274	0.83[ASN][1000 genomes]
rs12987967	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13021606	0.84[EUR][1000 genomes]
rs13386146	0.88[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs13391522	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs13391803	0.93[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13399656	0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs13403284	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs13407214	0.85[ASN][1000 genomes]
rs13428703	0.93[CEU][hapmap]
rs13432302	0.83[ASN][1000 genomes]
rs17039558	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs17045939	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs17046061	0.83[EUR][1000 genomes]
rs17046067	0.83[EUR][1000 genomes]
rs17046077	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs17046108	0.93[CEU][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes]
rs17046257	0.88[CHB][hapmap]
rs2048370	0.86[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs2229503	0.93[CEU][hapmap];0.88[CHB][hapmap];0.85[EUR][1000 genomes]
rs2271329	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs28581481	0.82[ASN][1000 genomes]
rs2971886	0.82[AFR][1000 genomes]
rs3287	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs34077590	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34094680	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34308676	0.81[EUR][1000 genomes]
rs34311770	0.83[EUR][1000 genomes]
rs34978408	0.85[EUR][1000 genomes]
rs35619551	0.82[EUR][1000 genomes]
rs3739109	0.93[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes]
rs3796017	0.83[ASN][1000 genomes]
rs3796018	0.83[ASN][1000 genomes]
rs3796019	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs3850350	0.81[EUR][1000 genomes]
rs4261758	0.85[CEU][hapmap]
rs4346422	0.88[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4347868	0.86[ASN][1000 genomes]
rs4358162	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4374410	0.88[ASN][1000 genomes]
rs4455200	0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4519566	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4577321	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4616509	0.83[ASN][1000 genomes]
rs4641979	0.83[ASN][1000 genomes]
rs57281248	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58419243	0.83[EUR][1000 genomes]
rs6545430	0.93[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs6545435	0.93[CEU][hapmap];0.88[CHB][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6545440	0.86[CEU][hapmap]
rs6706263	0.88[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs6708082	0.93[CEU][hapmap]
rs6721612	0.84[EUR][1000 genomes]
rs67244067	0.86[EUR][1000 genomes]
rs6730876	0.84[EUR][1000 genomes]
rs6734445	0.93[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6734536	0.93[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6739140	0.86[ASN][1000 genomes]
rs6741053	0.80[EUR][1000 genomes]
rs6749802	0.86[ASN][1000 genomes]
rs6752720	0.93[CEU][hapmap]
rs6753004	0.86[CEU][hapmap]
rs72806653	0.93[EUR][1000 genomes]
rs7340302	0.88[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7424459	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7556752	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7564719	0.85[ASN][1000 genomes]
rs7569127	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7582640	0.86[CEU][hapmap]
rs7584223	0.93[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7586066	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7586311	0.83[ASN][1000 genomes]
rs7599241	0.88[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7602992	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7608414	0.88[CHB][hapmap]

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
rs6724136	EML6	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54824800-54839200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr2:54827200-54839000	Weak transcription	Hela-S3	cervix
3	chr2:54827600-54839200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:54827600-54839200	Weak transcription	Dnd41	blood
5	chr2:54829800-54859800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:54830800-54839200	Weak transcription	Esophagus	oesophagus
7	chr2:54831000-54837800	Weak transcription	Osteobl	bone
8	chr2:54831200-54838000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:54832200-54838200	Enhancers	Brain Hippocampus Middle	brain
10	chr2:54832200-54839200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:54832200-54839200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:54832200-54839200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:54832200-54840800	Weak transcription	K562	blood
14	chr2:54832400-54839200	Weak transcription	Placenta	Placenta
15	chr2:54832400-54843400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:54832400-54843800	Weak transcription	Brain Germinal Matrix	brain
17	chr2:54832600-54839200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:54832800-54839000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr2:54832800-54839600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr2:54833000-54837800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:54833000-54839400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:54833000-54839400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:54833000-54839400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:54833000-54839600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:54833000-54841000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:54833400-54838800	Weak transcription	Primary B cells from cord blood	blood
27	chr2:54833400-54843400	Weak transcription	Fetal Brain Male	brain
28	chr2:54833600-54839200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:54833600-54839200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:54833600-54839200	Weak transcription	Psoas Muscle	Psoas
31	chr2:54833600-54839600	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:54833600-54840000	Weak transcription	Fetal Kidney	kidney
33	chr2:54833800-54837600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:54833800-54837800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:54833800-54838800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:54833800-54839200	Weak transcription	Thymus	Thymus
37	chr2:54833800-54839200	Weak transcription	NHEK	skin
38	chr2:54833800-54839200	Weak transcription	NHLF	lung
39	chr2:54833800-54840800	Weak transcription	HMEC	breast
40	chr2:54834000-54837600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:54834000-54837600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:54834000-54838200	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr2:54834000-54838600	Weak transcription	GM12878-XiMat	blood
44	chr2:54834000-54838800	Weak transcription	NH-A	brain
45	chr2:54834000-54839000	Weak transcription	Fetal Lung	lung
46	chr2:54834000-54839200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:54834000-54839200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:54834000-54839200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:54834000-54839200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:54834000-54839200	Weak transcription	Fetal Stomach	stomach

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