Variant report

Variant	rs4727924
Chromosome Location	chr7:121031879-121031880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:121028054..121033161-chr7:121034534..121038947,14	MCF-7	breast:
2	chr7:121031531..121033758-chr7:121126191..121127906,2	K562	blood:
3	chr7:121019447..121023769-chr7:121027958..121032895,6	MCF-7	breast:
4	chr7:121031761..121033507-chrX:23092305..23095304,2	K562	blood:
5	chr7:121031761..121034015-chrX:23093804..23095324,2	K562	blood:
6	chr7:121031207..121033515-chr7:121081375..121082898,2	K562	blood:

Variant related genes	Relation type
ENSG00000174028	Chromatin interaction
ENSG00000213310	Chromatin interaction
ENSG00000196937	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2244812	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270215	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536172	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536182	0.96[CEU][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes]
rs2536185	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536189	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2707466	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2908004	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3779381	0.90[JPT][hapmap]
rs3801387	0.90[JPT][hapmap]
rs718766	0.90[JPT][hapmap]
rs7776725	0.90[JPT][hapmap]
rs7793554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7807894	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917726	0.91[JPT][hapmap]
rs917727	0.90[JPT][hapmap]

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
rs4727924	FAM3C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

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	chr7:121005200-121035000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:121010200-121034600	Weak transcription	Fetal Brain Male	brain
5	chr7:121016000-121035400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr7:121016200-121035000	Weak transcription	Fetal Stomach	stomach
7	chr7:121016200-121035600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:121017600-121032400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:121018000-121035400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr7:121018600-121032400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr7:121018600-121032400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:121018600-121034600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr7:121018600-121034800	Weak transcription	Fetal Brain Female	brain
14	chr7:121018600-121034800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr7:121018600-121035600	Weak transcription	Gastric	stomach
16	chr7:121018800-121034400	Weak transcription	Liver	Liver
17	chr7:121018800-121035400	Weak transcription	Placenta	Placenta
18	chr7:121020000-121035400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr7:121020200-121035000	Weak transcription	Thymus	Thymus
20	chr7:121021400-121032600	Weak transcription	HMEC	breast
21	chr7:121021600-121034200	Weak transcription	Hela-S3	cervix
22	chr7:121022800-121032000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:121023400-121032400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr7:121024800-121035000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr7:121025600-121032400	Weak transcription	Lung	lung
26	chr7:121026200-121032200	Weak transcription	Fetal Muscle Leg	muscle
27	chr7:121026200-121032400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr7:121026200-121032400	Weak transcription	Osteobl	bone
29	chr7:121026200-121032600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr7:121026200-121034400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr7:121026200-121034600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr7:121026200-121034600	Weak transcription	Ovary	ovary
33	chr7:121026200-121034600	Weak transcription	A549	lung
34	chr7:121026200-121034800	Weak transcription	Brain Hippocampus Middle	brain
35	chr7:121026200-121035000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr7:121026200-121035000	Weak transcription	Brain Anterior Caudate	brain
37	chr7:121026200-121035000	Weak transcription	Fetal Kidney	kidney
38	chr7:121026200-121035400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr7:121026200-121035600	Weak transcription	Left Ventricle	heart
40	chr7:121026200-121035800	Weak transcription	Spleen	Spleen
41	chr7:121026400-121034400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr7:121026400-121034600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr7:121026400-121034600	Weak transcription	Colon Smooth Muscle	Colon
44	chr7:121026400-121034800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr7:121026600-121034400	Weak transcription	HUVEC	blood vessel
46	chr7:121026600-121034600	Weak transcription	Fetal Lung	lung
47	chr7:121026600-121034800	Weak transcription	Adipose Nuclei	Adipose
48	chr7:121026600-121034800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr7:121026600-121035000	Weak transcription	HSMMtube	muscle
50	chr7:121026600-121035400	Weak transcription	Pancreas	Pancrea

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