Variant report

Variant	rs718766
Chromosome Location	chr7:121025502-121025503
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:121024160..121027872-chr7:121035173..121037761,6	MCF-7	breast:
2	chr7:121024298..121027882-chr7:121032352..121035031,6	MCF-7	breast:
3	chr7:121022125..121023837-chr7:121025372..121027321,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196937	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10242100	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171617	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12531355	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539772	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254595	0.90[JPT][hapmap]
rs2536180	0.90[JPT][hapmap]
rs2536182	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2536189	0.90[JPT][hapmap]
rs2707466	0.90[JPT][hapmap]
rs28395249	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2908004	0.90[JPT][hapmap]
rs3779381	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801382	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801383	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801387	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727924	0.90[JPT][hapmap]
rs55963900	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56364616	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776725	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793554	0.90[JPT][hapmap]
rs7801915	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807953	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808155	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs917727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1034353	chr7:120818382-121040576	Enhancers Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1026322	chr7:120841937-121188037	Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv539102	chr7:120841937-121188037	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2755350	chr7:120848049-121119049	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1032054	chr7:120926379-121432971	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv539103	chr7:120926379-121432971	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs718766	FAM3C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120979800-121034800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr7:120984200-121035000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr7:120986200-121029600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:120986400-121026000	Weak transcription	Colonic Mucosa	Colon
5	chr7:120986400-121026000	Weak transcription	Psoas Muscle	Psoas
6	chr7:120993000-121025600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr7:120995600-121026200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:121000800-121029600	Weak transcription	Brain Angular Gyrus	brain
9	chr7:121001000-121026000	Weak transcription	Aorta	Aorta
10	chr7:121002400-121025800	Weak transcription	Brain Hippocampus Middle	brain
11	chr7:121005000-121030600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:121005200-121035000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr7:121010200-121034600	Weak transcription	Fetal Brain Male	brain
14	chr7:121015800-121025600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:121016000-121035400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:121016200-121035000	Weak transcription	Fetal Stomach	stomach
17	chr7:121016200-121035600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:121016400-121026000	Weak transcription	NHLF	lung
19	chr7:121017200-121026000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr7:121017600-121032400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr7:121018000-121025600	Weak transcription	Fetal Kidney	kidney
22	chr7:121018000-121025800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr7:121018000-121025800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr7:121018000-121035400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr7:121018400-121031600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:121018600-121025600	Weak transcription	Adipose Nuclei	Adipose
27	chr7:121018600-121025800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr7:121018600-121032400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:121018600-121032400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:121018600-121034600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr7:121018600-121034800	Weak transcription	Fetal Brain Female	brain
32	chr7:121018600-121034800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr7:121018600-121035600	Weak transcription	Gastric	stomach
34	chr7:121018800-121028600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr7:121018800-121034400	Weak transcription	Liver	Liver
36	chr7:121018800-121035400	Weak transcription	Placenta	Placenta
37	chr7:121019600-121025800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr7:121019800-121025600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:121020000-121026000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr7:121020000-121035400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr7:121020200-121031400	Weak transcription	K562	blood
42	chr7:121020200-121035000	Weak transcription	Thymus	Thymus
43	chr7:121020400-121025800	Weak transcription	Dnd41	blood
44	chr7:121021200-121028800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr7:121021400-121030800	Weak transcription	NHEK	skin
46	chr7:121021400-121032600	Weak transcription	HMEC	breast
47	chr7:121021600-121034200	Weak transcription	Hela-S3	cervix
48	chr7:121022000-121025600	Weak transcription	NHDF-Ad	bronchial
49	chr7:121022200-121031400	Enhancers	Primary B cells from cord blood	blood
50	chr7:121022200-121031600	Weak transcription	HepG2	liver

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