Variant report

Variant	rs7778413
Chromosome Location	chr7:127357716-127357717
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr7:127357650-127357799	MCF10A-Er-Src	breast:	n/a	chr7:127357733-127357742
2	RUNX3	chr7:127357477-127357945	GM12878	blood:	n/a	chr7:127357580-127357589 chr7:127357580-127357589
3	POLR2A	chr7:127357689-127357957	K562	blood:	n/a	n/a
4	POLR2A	chr7:127357370-127357750	K562	blood:	n/a	n/a
5	POLR2A	chr7:127357557-127357749	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:127357441-127357768	K562	blood:	n/a	n/a
7	GATA1	chr7:127357685-127358700	PBDE	blood:	n/a	n/a

Variant related genes	Relation type
SND1	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10229165	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10229583	1.00[CHB][hapmap]
rs10238047	0.92[EUR][1000 genomes]
rs10239440	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10249616	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10265516	0.90[ASN][1000 genomes]
rs10270127	0.94[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes]
rs10280863	0.90[ASN][1000 genomes]
rs11765620	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11767317	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11773160	0.93[ASN][1000 genomes]
rs1440971	0.92[EUR][1000 genomes]
rs1440972	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808089	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4473953	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57103099	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6467152	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6943219	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6943385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6946292	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6947779	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6953134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965698	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6969353	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6976887	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6979634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73450923	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7781189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs7783102	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7783478	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7784200	0.88[ASW][hapmap];0.88[CHB][hapmap]
rs7786786	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7792695	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7801118	0.86[EUR][1000 genomes]
rs806176	0.83[CHB][hapmap]
rs806178	0.83[CHB][hapmap]
rs806179	0.94[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.87[EUR][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	nsv831122	chr7:127143207-127357885	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1031658	chr7:127266882-127376775	Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv831123	chr7:127289511-127510396	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1030387	chr7:127348973-127455890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7778413	C7orf54	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127324800-127372200	Weak transcription	Fetal Heart	heart
2	chr7:127325600-127363000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:127326600-127379800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr7:127326800-127371000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:127331600-127375600	Strong transcription	Fetal Thymus	thymus
6	chr7:127334400-127376600	Weak transcription	Fetal Brain Male	brain
7	chr7:127335000-127359400	Strong transcription	Hela-S3	cervix
8	chr7:127339400-127371000	Weak transcription	Right Atrium	heart
9	chr7:127344600-127371200	Weak transcription	Brain Germinal Matrix	brain
10	chr7:127345000-127362000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr7:127345400-127361000	Weak transcription	Colonic Mucosa	Colon
12	chr7:127347800-127365200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:127347800-127383000	Strong transcription	NHEK	skin
14	chr7:127348600-127357800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr7:127349000-127360400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr7:127349400-127358200	Weak transcription	Pancreas	Pancrea
17	chr7:127349600-127360400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:127349600-127371200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:127350600-127358200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr7:127351400-127358000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr7:127351400-127361000	Weak transcription	Ovary	ovary
22	chr7:127351400-127361200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr7:127351400-127362600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr7:127351400-127365800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr7:127351400-127365800	Strong transcription	HSMM	muscle
26	chr7:127351400-127366200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr7:127351400-127368400	Weak transcription	Stomach Mucosa	stomach
28	chr7:127351400-127375600	Strong transcription	Liver	Liver
29	chr7:127351400-127383800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr7:127351600-127382200	Strong transcription	K562	blood
31	chr7:127351800-127360800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr7:127351800-127361600	Weak transcription	Colon Smooth Muscle	Colon
33	chr7:127351800-127371000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:127352000-127364800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:127352200-127372400	Strong transcription	HepG2	liver
36	chr7:127352600-127375600	Strong transcription	Primary T cells from cord blood	blood
37	chr7:127352800-127358200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:127352800-127358800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr7:127352800-127370400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr7:127354000-127370400	Weak transcription	Brain Angular Gyrus	brain
41	chr7:127354200-127357800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr7:127354200-127357800	Weak transcription	Fetal Intestine Small	intestine
43	chr7:127354200-127358800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:127354200-127360200	Weak transcription	Brain Substantia Nigra	brain
45	chr7:127354200-127365200	Weak transcription	Brain Hippocampus Middle	brain
46	chr7:127354200-127365400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr7:127354200-127368400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:127354200-127368400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr7:127354200-127370600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr7:127354200-127374000	Weak transcription	Fetal Brain Female	brain

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