Variant report

Variant	rs12505696
Chromosome Location	chr4:89931070-89931071
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10031518	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10433949	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs10470936	0.83[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11097216	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11722033	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11725475	0.86[ASN][1000 genomes]
rs11725938	0.81[ASN][1000 genomes]
rs11726708	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12505427	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507131	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12508371	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12508524	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12509305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs13129885	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13146548	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1398942	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1533292	0.86[CHD][hapmap];0.88[JPT][hapmap]
rs1533293	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3733448	0.88[JPT][hapmap]
rs4367140	0.86[CHD][hapmap];0.88[JPT][hapmap]
rs4627822	0.86[CHD][hapmap];0.88[JPT][hapmap]
rs59684168	0.84[ASN][1000 genomes]
rs60770708	0.82[ASN][1000 genomes]
rs61315828	0.84[ASN][1000 genomes]
rs67850063	0.95[ASN][1000 genomes]
rs6817766	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs6838424	0.92[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7691363	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9307058	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9790655	0.88[ASN][1000 genomes]
rs9994655	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv998651	chr4:89800245-89933445	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv537175	chr4:89800245-89933445	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12505696	FAM13A	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89896800-89934800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr4:89903000-89957200	Weak transcription	HSMM	muscle
3	chr4:89903400-89936000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:89909800-89931200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:89912200-89935800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:89912200-89943800	Weak transcription	Psoas Muscle	Psoas
7	chr4:89913400-89944000	Weak transcription	Gastric	stomach
8	chr4:89920400-89937000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:89921000-89950600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr4:89922400-89936000	Weak transcription	Adipose Nuclei	Adipose
11	chr4:89922600-89932600	Weak transcription	NHDF-Ad	bronchial
12	chr4:89922600-89935000	Weak transcription	Placenta	Placenta
13	chr4:89922600-89936800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:89922600-89949800	Weak transcription	HMEC	breast
15	chr4:89922800-89931800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:89922800-89935800	Weak transcription	HUVEC	blood vessel
17	chr4:89922800-89945600	Weak transcription	A549	lung
18	chr4:89923000-89932200	Weak transcription	Osteobl	bone
19	chr4:89923000-89935000	Weak transcription	Fetal Kidney	kidney
20	chr4:89923400-89939400	Weak transcription	Primary T cells from cord blood	blood
21	chr4:89923600-89945600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:89923800-89936000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:89923800-89936000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:89923800-89937000	Weak transcription	Fetal Heart	heart
25	chr4:89923800-89943800	Weak transcription	Right Atrium	heart
26	chr4:89923800-89944400	Weak transcription	Colon Smooth Muscle	Colon
27	chr4:89924400-89934000	Weak transcription	Fetal Brain Female	brain
28	chr4:89925000-89931600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:89925400-89937000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr4:89925600-89939400	Weak transcription	Aorta	Aorta
31	chr4:89926000-89936000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:89926200-89936400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:89926400-89933600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:89926400-89949600	Weak transcription	Left Ventricle	heart
35	chr4:89926600-89941000	Weak transcription	Esophagus	oesophagus
36	chr4:89926800-89935200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:89926800-89951400	Weak transcription	Right Ventricle	heart
38	chr4:89927400-89932800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr4:89927600-89931400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:89928000-89931800	Weak transcription	Pancreas	Pancrea
41	chr4:89928000-89935000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:89928200-89936000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:89928400-89931200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:89928400-89936400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr4:89928400-89940000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:89928600-89932200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:89928600-89932400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr4:89928600-89934200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:89928600-89934800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:89928600-89934800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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