Variant report

Variant	rs453670
Chromosome Location	chr10:61123193-61123194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr10:61121822-61123262	H1-neurons	neurons:	n/a	n/a
2	TCF12	chr10:61121337-61123350	SK-N-SH	brain:	n/a	chr10:61122968-61122976
3	TCF12	chr10:61122964-61123210	H1-hESC	embryonic stem cell:	n/a	chr10:61122968-61122976
4	POLR2A	chr10:61121418-61123376	H1-neurons	neurons:	n/a	n/a
5	REST	chr10:61120382-61123691	H1-neurons	neurons:	n/a	chr10:61120572-61120585
6	MXI1	chr10:61120315-61123441	SK-N-SH	brain:	n/a	chr10:61122817-61122832
7	E2F4	chr10:61122906-61123264	MCF10A-Er-Src	breast:	n/a	n/a
8	TAF1	chr10:61121744-61123292	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr10:61121476-61123366	H1-neurons	neurons:	n/a	n/a
10	TAF1	chr10:61122740-61123246	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
FAM13C	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1824429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1901179	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs284602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs284610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs284614	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs284633	1.00[JPT][hapmap]
rs397014	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs410191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv831888	chr10:60943655-61138251	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv467289	chr10:61075213-61139869	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv551148	chr10:61075213-61139869	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv551149	chr10:61115114-61190125	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs453670	FAM13C	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:61119600-61123600	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr10:61120000-61123200	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr10:61120400-61123200	Active TSS	Aorta	Aorta
4	chr10:61120400-61123400	Active TSS	Brain Anterior Caudate	brain
5	chr10:61120400-61123600	Active TSS	Brain Angular Gyrus	brain
6	chr10:61120400-61123600	Active TSS	Brain Hippocampus Middle	brain
7	chr10:61120400-61123600	Active TSS	Fetal Brain Female	brain
8	chr10:61120600-61123200	Active TSS	Brain Germinal Matrix	brain
9	chr10:61120800-61123200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr10:61120800-61123200	Active TSS	Right Atrium	heart
11	chr10:61121000-61123200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr10:61121000-61123200	Active TSS	Fetal Heart	heart
13	chr10:61121000-61123200	Active TSS	Ovary	ovary
14	chr10:61121000-61123200	Active TSS	Psoas Muscle	Psoas
15	chr10:61121000-61123800	Active TSS	Fetal Brain Male	brain
16	chr10:61121200-61123200	Active TSS	Colon Smooth Muscle	Colon
17	chr10:61121200-61123200	Active TSS	Rectal Smooth Muscle	rectum
18	chr10:61121200-61123200	Active TSS	HSMMtube	muscle
19	chr10:61121200-61123400	Active TSS	Stomach Smooth Muscle	stomach
20	chr10:61121200-61123600	Active TSS	Brain Cingulate Gyrus	brain
21	chr10:61121600-61123200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr10:61121600-61123200	Active TSS	Colonic Mucosa	Colon
23	chr10:61121600-61123200	Active TSS	Left Ventricle	heart
24	chr10:61121800-61123200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr10:61121800-61123200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr10:61121800-61123200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr10:61121800-61123200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr10:61121800-61123200	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr10:61122000-61123200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr10:61122000-61123200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
31	chr10:61122000-61123200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr10:61122000-61123200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
33	chr10:61122000-61123200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
34	chr10:61122000-61123200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr10:61122000-61123200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr10:61122000-61123200	Active TSS	Muscle Satellite Cultured Cells	--
37	chr10:61122000-61123200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
38	chr10:61122000-61123200	Active TSS	NH-A	brain
39	chr10:61122200-61123200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr10:61122400-61123200	Active TSS	H1 Cell Line	embryonic stem cell
41	chr10:61122400-61123200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
42	chr10:61122400-61123200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr10:61122400-61123200	Active TSS	Adipose Nuclei	Adipose
44	chr10:61122400-61123200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
45	chr10:61122600-61123200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
46	chr10:61122600-61123200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr10:61122600-61123200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr10:61122600-61123200	Enhancers	Placenta	Placenta
49	chr10:61122800-61123200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr10:61122800-61123200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell

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