Variant report

Variant	rs4678420
Chromosome Location	chr3:138185860-138185861
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138185730..138189738-chr3:138190908..138194397,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158220	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1082037	0.86[ASN][1000 genomes]
rs1088055	0.86[ASN][1000 genomes]
rs1091528	0.80[CEU][hapmap]
rs10935284	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709290	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs13101081	1.00[ASN][1000 genomes]
rs1379257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1479930	1.00[ASN][1000 genomes]
rs1600511	1.00[ASN][1000 genomes]
rs1630766	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1673593	0.86[ASN][1000 genomes]
rs1673607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1673624	0.80[ASN][1000 genomes]
rs1679167	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1679168	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679175	0.93[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1720836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2347469	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607795	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2881793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3813264	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs4432674	0.86[ASN][1000 genomes]
rs4678264	1.00[ASN][1000 genomes]
rs4678265	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550507	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs559313	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs586946	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs60513493	0.86[ASN][1000 genomes]
rs611134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs629884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs643620	0.81[CEU][hapmap]
rs6798058	0.80[ASN][1000 genomes]
rs680070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7625326	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7634745	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7643973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7653815	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs773444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs773445	0.86[ASN][1000 genomes]
rs774003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs774004	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs774005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774006	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774007	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774008	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs808925	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs811792	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs811793	1.00[ASN][1000 genomes]
rs9811052	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9817419	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9827256	0.93[ASN][1000 genomes]
rs9848718	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9848938	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9853998	1.00[ASN][1000 genomes]
rs9878436	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9879213	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv460864	chr3:138100539-138194435	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv591853	chr3:138100539-138194435	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv522517	chr3:138174523-138297982	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4678420	CEP70	cis	Muscle Skeletal	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138161600-138198400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:138170800-138198400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:138171000-138193000	Weak transcription	Pancreas	Pancrea
4	chr3:138171400-138198400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:138175200-138196000	Weak transcription	Brain Anterior Caudate	brain
6	chr3:138176800-138187200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:138177600-138187200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:138177600-138195400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:138178000-138197000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:138178200-138196000	Weak transcription	Aorta	Aorta
11	chr3:138178600-138187000	Weak transcription	Right Atrium	heart
12	chr3:138178800-138188800	Weak transcription	Right Ventricle	heart
13	chr3:138179800-138188600	Weak transcription	Fetal Intestine Small	intestine
14	chr3:138179800-138199400	Weak transcription	Thymus	Thymus
15	chr3:138180800-138187400	Weak transcription	NHDF-Ad	bronchial
16	chr3:138181000-138187600	Weak transcription	HSMM	muscle
17	chr3:138181200-138192400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:138182800-138187400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:138182800-138187800	Strong transcription	Lung	lung
20	chr3:138183200-138187600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:138183400-138186400	Weak transcription	Psoas Muscle	Psoas
22	chr3:138183600-138187000	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:138184400-138186200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:138184400-138187000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:138184400-138188200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:138184400-138191200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:138184400-138198400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:138184600-138186200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:138184600-138186200	Weak transcription	Fetal Stomach	stomach
30	chr3:138184800-138186400	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:138185000-138186400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:138185000-138187400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:138185000-138195200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:138185200-138186000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:138185200-138186600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:138185200-138187200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:138185400-138189600	Strong transcription	Fetal Muscle Trunk	muscle
38	chr3:138185600-138186000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:138185600-138187800	Weak transcription	HSMMtube	muscle

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