Variant report

Variant	rs4319969
Chromosome Location	chr2:54755878-54755879
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	chr2:54754602..54758699-chr2:54783105..54787010,4	MCF-7	breast:
2	chr2:54749132..54757147-chr2:54784492..54789269,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10170355	0.89[CHB][hapmap]
rs10176359	0.89[CHB][hapmap]
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	0.80[EUR][1000 genomes]
rs1137645	0.89[CHB][hapmap]
rs11555856	0.83[EUR][1000 genomes]
rs11883910	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11892236	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap]
rs11892443	1.00[CHB][hapmap]
rs11902987	1.00[CHB][hapmap]
rs11904679	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12713264	0.89[CHB][hapmap]
rs12713265	0.89[CHB][hapmap]
rs12713268	0.89[CHB][hapmap]
rs12713269	0.89[CHB][hapmap]
rs12713273	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs12987967	0.84[EUR][1000 genomes]
rs13006815	0.83[EUR][1000 genomes]
rs13021615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13036147	0.86[EUR][1000 genomes]
rs13386146	0.89[CHB][hapmap]
rs13391522	0.89[CHB][hapmap]
rs13391803	0.86[CEU][hapmap];0.88[CHB][hapmap];0.81[EUR][1000 genomes]
rs13399656	0.88[CHB][hapmap]
rs13403284	0.89[CHB][hapmap]
rs17039558	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17045939	0.92[CEU][hapmap];0.89[CHB][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes]
rs17046077	1.00[YRI][hapmap]
rs17046108	0.91[YRI][hapmap]
rs17046257	0.89[CHB][hapmap]
rs2229503	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs2271329	1.00[YRI][hapmap]
rs3287	0.89[CHB][hapmap]
rs34077590	0.84[EUR][1000 genomes]
rs34094680	0.84[EUR][1000 genomes]
rs34263579	0.98[AFR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34308676	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34429083	0.87[EUR][1000 genomes]
rs34978408	0.84[EUR][1000 genomes]
rs36018286	0.87[EUR][1000 genomes]
rs3739109	0.88[CHB][hapmap];1.00[YRI][hapmap]
rs3796019	0.89[CHB][hapmap]
rs3796022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4261758	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4346422	0.89[CHB][hapmap]
rs4455200	0.88[CHB][hapmap]
rs45487791	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57281248	0.84[EUR][1000 genomes]
rs61126015	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545430	0.86[CEU][hapmap];0.89[CHB][hapmap]
rs6545435	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs66693131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706263	0.88[CHB][hapmap]
rs6734445	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs6734536	0.86[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs7340302	0.89[CHB][hapmap]
rs7556752	0.89[CHB][hapmap]
rs7569127	0.89[CHB][hapmap]
rs7584223	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs7586066	0.81[EUR][1000 genomes]
rs7599241	0.89[CHB][hapmap]
rs7608414	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	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
3	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
5	nsv961776	chr2:54755470-54757189	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4319969	EML6	cis	Thyroid	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
2	chr2:54740600-54761800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
5	chr2:54746600-54758400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:54747000-54760600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:54747200-54761800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:54748400-54768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
11	chr2:54750600-54757000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:54750800-54759200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:54750800-54769800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:54751000-54756800	Weak transcription	Fetal Intestine Large	intestine
15	chr2:54751000-54759400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:54751000-54759600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:54751000-54760200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:54752000-54756200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:54752000-54760200	Weak transcription	Colonic Mucosa	Colon
20	chr2:54752000-54764600	Weak transcription	Gastric	stomach
21	chr2:54752200-54759600	Weak transcription	Small Intestine	intestine
22	chr2:54752200-54767600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:54752400-54757000	Weak transcription	Hela-S3	cervix
25	chr2:54752400-54758000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:54752400-54758000	Weak transcription	Aorta	Aorta
27	chr2:54752400-54758000	Weak transcription	NHEK	skin
28	chr2:54752400-54758200	Weak transcription	Fetal Thymus	thymus
29	chr2:54752400-54759600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:54752600-54758000	Weak transcription	HMEC	breast
31	chr2:54752600-54758600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:54752600-54759800	Weak transcription	GM12878-XiMat	blood
33	chr2:54753000-54758800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:54753000-54759000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:54753200-54756200	Strong transcription	HepG2	liver
36	chr2:54753200-54756400	Genic enhancers	HSMMtube	muscle
37	chr2:54753200-54756800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:54753200-54756800	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:54753200-54757000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:54753200-54757400	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr2:54753200-54757400	Strong transcription	Fetal Brain Female	brain
42	chr2:54753200-54758000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:54753200-54758200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:54753200-54759800	Strong transcription	Adipose Nuclei	Adipose
45	chr2:54753400-54756800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:54753400-54757200	Strong transcription	HUVEC	blood vessel
47	chr2:54753400-54757400	Strong transcription	NHDF-Ad	bronchial
48	chr2:54753400-54757600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:54753400-54758600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:54753400-54758800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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