Variant report

Variant	rs917727
Chromosome Location	chr7:121018579-121018580
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:121017884..121020146-chr7:121086694..121088827,2	K562	blood:
2	chr7:121016002..121021712-chr7:121034134..121038375,6	MCF-7	breast:
3	chr7:121012261..121016480-chr7:121017791..121020444,4	K562	blood:
4	chr7:121018164..121019709-chr7:121020264..121022933,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196937	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10242100	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171617	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12531355	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539772	0.86[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	0.87[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];0.90[MEX][hapmap];0.95[TSI][hapmap];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];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801383	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727924	0.90[JPT][hapmap]
rs55963900	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56364616	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718766	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]
rs7776725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793554	0.90[JPT][hapmap]
rs7801915	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807953	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808155	0.86[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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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

Variant related diseases (count:1)

Disease	PMID	Source
Bone mineral density	22792070	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs917727	FAM3C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120970600-121025400	Weak transcription	Spleen	Spleen
2	chr7:120979800-121019400	Weak transcription	Thymus	Thymus
3	chr7:120979800-121034800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr7:120980800-121019600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:120984200-121035000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr7:120986200-121029600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:120986400-121026000	Weak transcription	Colonic Mucosa	Colon
8	chr7:120986400-121026000	Weak transcription	Psoas Muscle	Psoas
9	chr7:120993000-121025600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr7:120995600-121026200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:121000000-121024200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:121000800-121029600	Weak transcription	Brain Angular Gyrus	brain
13	chr7:121001000-121026000	Weak transcription	Aorta	Aorta
14	chr7:121001800-121023200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr7:121002000-121023000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr7:121002200-121022000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr7:121002200-121025400	Weak transcription	Right Ventricle	heart
18	chr7:121002400-121020400	Weak transcription	Brain Germinal Matrix	brain
19	chr7:121002400-121025800	Weak transcription	Brain Hippocampus Middle	brain
20	chr7:121005000-121024000	Weak transcription	Stomach Mucosa	stomach
21	chr7:121005000-121030600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr7:121005200-121035000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr7:121005800-121023200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:121008600-121020400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:121008600-121025400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr7:121009400-121023400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:121009800-121025400	Weak transcription	Right Atrium	heart
28	chr7:121010200-121034600	Weak transcription	Fetal Brain Male	brain
29	chr7:121010400-121023800	Weak transcription	Fetal Intestine Small	intestine
30	chr7:121010400-121025400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr7:121013200-121021000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:121013200-121024600	Weak transcription	Colon Smooth Muscle	Colon
33	chr7:121013400-121020200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:121013400-121022000	Genic enhancers	Primary B cells from cord blood	blood
35	chr7:121013400-121023400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr7:121013600-121018800	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr7:121013600-121020800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr7:121013600-121021600	Weak transcription	Fetal Heart	heart
39	chr7:121013600-121023000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr7:121013600-121024200	Strong transcription	HSMM	muscle
41	chr7:121014000-121023600	Strong transcription	NH-A	brain
42	chr7:121014000-121023800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr7:121014400-121018600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:121014400-121019600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr7:121014400-121019600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr7:121014600-121018600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr7:121014600-121020400	Strong transcription	Dnd41	blood
48	chr7:121014600-121021400	Strong transcription	Osteobl	bone
49	chr7:121015000-121018600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr7:121015000-121018800	Strong transcription	Rectal Mucosa Donor 31	rectum

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