Variant report

Variant	rs646929
Chromosome Location	chr3:54695763-54695764
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11130431	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs4353779	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs517729	0.81[CHB][hapmap]
rs578032	0.85[GIH][hapmap]
rs667671	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs838022	0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs646929	FAM116A	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54685200-54704000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:54689200-54697200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:54691400-54704000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:54693400-54697800	Weak transcription	Right Atrium	heart
5	chr3:54693400-54702400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:54693600-54699200	Enhancers	Fetal Muscle Leg	muscle
7	chr3:54693800-54696600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:54694000-54702200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:54694000-54702400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:54694000-54702600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:54694000-54702800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:54694600-54695800	Enhancers	Brain Anterior Caudate	brain
13	chr3:54694600-54696200	Enhancers	Fetal Stomach	stomach
14	chr3:54694800-54697200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:54695200-54697200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:54695200-54697800	Weak transcription	Psoas Muscle	Psoas
17	chr3:54695200-54703200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:54695400-54696000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:54695400-54697000	Weak transcription	Fetal Kidney	kidney
20	chr3:54695400-54697600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:54695400-54697600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:54695400-54697800	Weak transcription	Spleen	Spleen
23	chr3:54695400-54698200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:54695400-54703800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:54695600-54696000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:54695600-54697800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:54695600-54702200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:54695600-54704000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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