Variant report

Variant	rs11904679
Chromosome Location	chr2:54766158-54766159
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54764232..54766337-chr2:54769153..54772806,3	K562	blood:
2	chr2:54764181..54766561-chr2:54813594..54815881,2	K562	blood:
3	chr2:54761550..54763887-chr2:54765151..54767469,2	K562	blood:
4	chr2:54764431..54771229-chr2:54784220..54787609,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10169439	1.00[CEU][hapmap]
rs10170355	0.89[CHB][hapmap]
rs10176359	0.92[CEU][hapmap];0.89[CHB][hapmap];0.82[EUR][1000 genomes]
rs10176445	0.89[CHB][hapmap]
rs10182836	0.89[CHB][hapmap]
rs10183867	0.89[CHB][hapmap]
rs10184128	0.89[CHB][hapmap]
rs10188185	0.85[CHB][hapmap]
rs10193692	0.88[CHB][hapmap]
rs10205410	1.00[CHB][hapmap]
rs10206143	0.89[CHB][hapmap]
rs10528	1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs1137645	0.89[CHB][hapmap]
rs11555856	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11892236	0.90[CEU][hapmap];0.84[CHB][hapmap]
rs11892443	1.00[CHB][hapmap]
rs11896957	0.90[EUR][1000 genomes]
rs11902659	0.82[EUR][1000 genomes]
rs11902987	1.00[CHB][hapmap]
rs12713264	0.89[CHB][hapmap]
rs12713265	0.89[CHB][hapmap]
rs12713268	0.89[CHB][hapmap]
rs12713269	0.89[CHB][hapmap]
rs12713270	0.86[EUR][1000 genomes]
rs12713271	0.86[EUR][1000 genomes]
rs12713272	0.82[EUR][1000 genomes]
rs12713273	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs12987967	0.86[EUR][1000 genomes]
rs13004944	0.84[EUR][1000 genomes]
rs13006815	0.82[EUR][1000 genomes]
rs13021606	0.90[EUR][1000 genomes]
rs13021615	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13036147	0.85[EUR][1000 genomes]
rs13386146	0.89[CHB][hapmap]
rs13391522	0.89[CHB][hapmap]
rs13391803	0.85[CEU][hapmap];0.88[CHB][hapmap];0.83[EUR][1000 genomes]
rs13399656	0.88[CHB][hapmap]
rs13403284	0.89[CHB][hapmap]
rs13428703	0.85[CEU][hapmap]
rs17039558	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17045939	0.92[CEU][hapmap];0.89[CHB][hapmap];0.85[EUR][1000 genomes]
rs17046036	0.84[EUR][1000 genomes]
rs17046108	0.83[TSI][hapmap]
rs17046257	0.89[CHB][hapmap]
rs2229503	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs3287	0.89[CHB][hapmap]
rs34077590	0.86[EUR][1000 genomes]
rs34094680	0.85[EUR][1000 genomes]
rs34263579	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34308676	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34429083	0.86[EUR][1000 genomes]
rs34978408	0.85[EUR][1000 genomes]
rs36018286	0.87[EUR][1000 genomes]
rs3739109	0.88[CHB][hapmap]
rs3796019	0.89[CHB][hapmap]
rs3796022	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4261758	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4319969	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4346422	0.89[CHB][hapmap]
rs4358162	0.86[EUR][1000 genomes]
rs4455200	0.88[CHB][hapmap]
rs45487791	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57281248	0.86[EUR][1000 genomes]
rs61126015	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6545430	0.85[CEU][hapmap];0.89[CHB][hapmap];0.81[EUR][1000 genomes]
rs6545435	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap]
rs6545440	0.85[CEU][hapmap]
rs66693131	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6706263	0.88[CHB][hapmap]
rs67079536	0.91[EUR][1000 genomes]
rs6708082	0.85[CEU][hapmap]
rs6710809	0.85[JPT][hapmap];0.85[MEX][hapmap]
rs6721612	0.90[EUR][1000 genomes]
rs67244067	0.85[EUR][1000 genomes]
rs6730876	0.90[EUR][1000 genomes]
rs6734445	0.85[CEU][hapmap];0.89[CHB][hapmap];0.81[EUR][1000 genomes]
rs6734536	0.85[CEU][hapmap];0.89[CHB][hapmap];0.85[EUR][1000 genomes]
rs6741053	0.86[EUR][1000 genomes]
rs6752720	0.85[CEU][hapmap]
rs6753004	0.85[CEU][hapmap]
rs7340302	0.89[CHB][hapmap]
rs7424459	0.81[EUR][1000 genomes]
rs7556752	0.89[CHB][hapmap]
rs7569127	0.92[CEU][hapmap];0.89[CHB][hapmap];0.82[EUR][1000 genomes]
rs7582640	0.85[CEU][hapmap]
rs7584223	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs7586066	0.83[EUR][1000 genomes]
rs7593062	0.85[JPT][hapmap];0.85[MEX][hapmap]
rs7599241	0.89[CHB][hapmap]
rs7608414	0.89[CHB][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11904679	EML6	cis	Thyroid	GTEx
rs11904679	C2orf63	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
2	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
4	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:54748400-54768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
7	chr2:54750800-54769800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:54752200-54767600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:54753800-54768200	Strong transcription	Fetal Muscle Leg	muscle
11	chr2:54754400-54767800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:54754800-54767800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:54755000-54767600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:54756800-54767600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:54757000-54767800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:54757000-54776800	Weak transcription	Brain Germinal Matrix	brain
17	chr2:54757400-54766200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:54757400-54771000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
20	chr2:54758600-54772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:54760200-54768800	Genic enhancers	Left Ventricle	heart
22	chr2:54760400-54769600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:54760600-54767000	Weak transcription	NH-A	brain
24	chr2:54760800-54767800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:54761000-54767000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:54761000-54769400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:54761200-54768800	Strong transcription	HSMM	muscle
28	chr2:54761600-54767200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:54761600-54773200	Weak transcription	Fetal Brain Male	brain
30	chr2:54761800-54769600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:54762000-54766800	Weak transcription	Right Ventricle	heart
32	chr2:54762000-54775400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:54762200-54770400	Weak transcription	Fetal Kidney	kidney
34	chr2:54762200-54772800	Weak transcription	Aorta	Aorta
35	chr2:54762200-54772800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:54762200-54773800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:54762400-54770800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr2:54762400-54772600	Weak transcription	Liver	Liver
39	chr2:54762600-54767000	Weak transcription	Brain Substantia Nigra	brain
40	chr2:54762600-54767200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr2:54762600-54767400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:54762800-54772600	Weak transcription	NHDF-Ad	bronchial
43	chr2:54763000-54767400	Weak transcription	HUVEC	blood vessel
44	chr2:54763000-54767600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr2:54763000-54776000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:54763200-54767000	Weak transcription	Fetal Heart	heart
47	chr2:54763200-54770800	Weak transcription	Fetal Intestine Small	intestine
48	chr2:54763200-54772600	Weak transcription	NHLF	lung
49	chr2:54763400-54767000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:54763400-54767000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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