Variant report

Variant	rs7701678
Chromosome Location	chr5:177553108-177553109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:177548762..177553216-chr5:177630602..177633012,4	MCF-7	breast:
2	chr5:177389362..177391423-chr5:177551819..177554278,2	MCF-7	breast:
3	chr5:177551780..177554441-chr5:177630455..177633730,4	MCF-7	breast:
4	chr5:177551974..177555394-chr5:177629147..177631755,4	K562	blood:

Variant related genes	Relation type
ENSG00000197451	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10035478	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10040895	0.83[ASN][1000 genomes]
rs10042021	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11952173	1.00[JPT][hapmap]
rs13180226	0.80[CEU][hapmap]
rs13189047	0.82[MEX][hapmap]
rs13436876	0.82[CHB][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36087128	0.83[EUR][1000 genomes]
rs3812074	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3812075	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3812079	0.88[ASW][hapmap];0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3812080	0.81[CEU][hapmap];0.91[GIH][hapmap]
rs4549545	1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap]
rs4637566	0.82[CHB][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6601217	0.94[GIH][hapmap]
rs6601220	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6873523	0.94[GIH][hapmap];0.88[MEX][hapmap]
rs6893797	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7379278	0.88[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7380934	0.82[ASW][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7380947	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7447860	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7710186	1.00[JPT][hapmap]
rs7732415	0.82[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030383	chr5:177310325-177571254	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
3	nsv1021198	chr5:177386267-177611648	Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
5	nsv462567	chr5:177505021-177572927	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv471058	chr5:177505021-177572927	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv600392	chr5:177505021-177572927	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
9	nsv883190	chr5:177532201-177620189	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	nsv883192	chr5:177535370-177564346	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv600394	chr5:177549491-177608195	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7701678	DCTN3	trans	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177541800-177557200	Weak transcription	Right Atrium	heart
2	chr5:177547000-177553400	Weak transcription	HUVEC	blood vessel
3	chr5:177548600-177557000	Weak transcription	Fetal Intestine Large	intestine
4	chr5:177548800-177557000	Weak transcription	Fetal Intestine Small	intestine
5	chr5:177548800-177557200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr5:177549200-177553600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr5:177549400-177554800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:177549400-177557200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr5:177549400-177558200	Weak transcription	Fetal Heart	heart
10	chr5:177549600-177557000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:177549600-177557200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:177549600-177557400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr5:177549800-177553400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:177550000-177553400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:177550200-177553600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:177550200-177554600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr5:177550200-177557000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:177550400-177556400	Weak transcription	GM12878-XiMat	blood
19	chr5:177550400-177557200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr5:177550600-177553600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:177550600-177553800	Weak transcription	Left Ventricle	heart
22	chr5:177550600-177557200	Weak transcription	Psoas Muscle	Psoas
23	chr5:177550800-177553600	Enhancers	K562	blood
24	chr5:177550800-177556800	Weak transcription	Primary B cells from cord blood	blood
25	chr5:177551200-177553400	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr5:177551200-177553400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:177551400-177556800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr5:177551400-177557400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr5:177551600-177553800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:177551600-177554200	Weak transcription	NHEK	skin
31	chr5:177551600-177557200	Weak transcription	Right Ventricle	heart
32	chr5:177551800-177553400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr5:177551800-177554400	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr5:177551800-177554800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr5:177551800-177556400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr5:177551800-177557000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr5:177551800-177557200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr5:177551800-177557400	Weak transcription	Spleen	Spleen
39	chr5:177552000-177553800	Weak transcription	Fetal Thymus	thymus
40	chr5:177552000-177554800	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr5:177552000-177557000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr5:177552000-177557200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr5:177552000-177557400	Weak transcription	Stomach Mucosa	stomach
44	chr5:177552200-177553200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:177552200-177553400	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr5:177552200-177553400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr5:177552200-177553800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr5:177552400-177553400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr5:177552400-177553600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr5:177552400-177555200	Weak transcription	Lung	lung

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