Variant report

Variant	rs2908004
Chromosome Location	chr7:120969769-120969770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120969341..120972493-chr7:120983934..120987124,3	K562	blood:
2	chr7:120969283..120970096-chr7:121634782..121635540,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2244812	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2254595	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2270215	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2536172	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2536180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2536182	0.92[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2536185	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2536189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2707466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3779381	0.90[JPT][hapmap]
rs3801387	0.90[JPT][hapmap]
rs4727924	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs718766	0.90[JPT][hapmap]
rs7776725	0.90[JPT][hapmap]
rs7793554	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7807894	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs917726	0.91[JPT][hapmap]
rs917727	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1027619	chr7:120906437-120976630	Enhancers Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	esv2757237	chr7:120908459-120993326	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	esv2759558	chr7:120908459-120993326	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active 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	4 gene(s)	inside rSNPs	diseases
9	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
10	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:2)

Disease	PMID	Source
Bone mineral density (paediatric, lower limb)	24945404	GWAS catalog
Bone mineral density	22792071	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2908004	FAM3C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120968600-120969800	Bivalent Enhancer	Placenta	Placenta
2	chr7:120968600-120970800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr7:120968600-120970800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr7:120968600-120971000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr7:120968600-120971000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr7:120968800-120969800	Enhancers	Gastric	stomach
7	chr7:120968800-120969800	Bivalent Enhancer	Psoas Muscle	Psoas
8	chr7:120968800-120970200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:120968800-120970200	Bivalent Enhancer	Fetal Brain Male	brain
10	chr7:120968800-120970200	Bivalent Enhancer	Fetal Heart	heart
11	chr7:120968800-120970200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
12	chr7:120968800-120970200	Bivalent/Poised TSS	HSMM	muscle
13	chr7:120968800-120970400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr7:120968800-120970400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr7:120968800-120970600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:120968800-120970600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
17	chr7:120968800-120970800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
18	chr7:120968800-120971000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
19	chr7:120968800-120971000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
20	chr7:120968800-120971000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr7:120969000-120969800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:120969000-120969800	Bivalent Enhancer	Adipose Nuclei	Adipose
23	chr7:120969000-120969800	Bivalent Enhancer	Liver	Liver
24	chr7:120969000-120969800	Flanking Active TSS	Right Ventricle	heart
25	chr7:120969000-120970000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
26	chr7:120969000-120970000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
27	chr7:120969000-120970000	Flanking Bivalent TSS/Enh	NH-A	brain
28	chr7:120969000-120970200	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr7:120969000-120970400	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr7:120969000-120970600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:120969000-120970600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
32	chr7:120969000-120970600	Flanking Bivalent TSS/Enh	NHEK	skin
33	chr7:120969000-120970800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr7:120969000-120970800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:120969000-120970800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr7:120969000-120970800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
37	chr7:120969000-120970800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
38	chr7:120969000-120970800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
39	chr7:120969000-120970800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
40	chr7:120969000-120971000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
41	chr7:120969000-120971000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
42	chr7:120969000-120971400	Bivalent/Poised TSS	NHDF-Ad	bronchial
43	chr7:120969200-120969800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
44	chr7:120969200-120969800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:120969200-120969800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
46	chr7:120969200-120969800	Bivalent Enhancer	Fetal Lung	lung
47	chr7:120969200-120970000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
48	chr7:120969200-120970000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
49	chr7:120969200-120970000	Flanking Bivalent TSS/Enh	HMEC	breast
50	chr7:120969200-120970600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood

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