Variant report

Variant	rs6835979
Chromosome Location	chr4:89912865-89912866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10004888	0.82[ASN][1000 genomes]
rs10006121	0.82[ASN][1000 genomes]
rs10009019	0.82[ASN][1000 genomes]
rs10023602	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10028596	0.82[ASN][1000 genomes]
rs10030965	0.82[ASN][1000 genomes]
rs10033484	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.83[ASN][1000 genomes]
rs10470886	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10470937	0.82[ASN][1000 genomes]
rs10856872	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1104633	0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs11097204	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11727482	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11737016	0.81[ASN][1000 genomes]
rs11737182	0.82[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.82[ASN][1000 genomes]
rs11936725	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12512799	0.83[ASN][1000 genomes]
rs12645240	0.81[ASN][1000 genomes]
rs1458557	0.88[CHD][hapmap];0.87[GIH][hapmap]
rs16996143	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs16996144	0.85[CEU][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1903006	0.81[ASN][1000 genomes]
rs1903007	0.81[ASN][1000 genomes]
rs1921679	0.88[CHD][hapmap];0.87[GIH][hapmap];0.80[ASN][1000 genomes]
rs1921681	0.85[CEU][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1921683	0.83[ASN][1000 genomes]
rs1921684	0.81[CHD][hapmap]
rs2085601	0.81[ASN][1000 genomes]
rs2178583	0.84[GIH][hapmap];0.81[ASN][1000 genomes]
rs2178584	0.88[CHD][hapmap];0.87[GIH][hapmap];0.81[ASN][1000 genomes]
rs2178585	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2609275	0.81[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2704573	0.82[CHB][hapmap]
rs2704574	0.81[ASN][1000 genomes]
rs2704576	0.81[ASN][1000 genomes]
rs2704577	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs28540701	0.82[ASN][1000 genomes]
rs2869972	0.82[JPT][hapmap]
rs2869973	0.83[ASN][1000 genomes]
rs2904262	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35232147	0.80[ASN][1000 genomes]
rs35441198	0.83[ASN][1000 genomes]
rs4507326	0.83[ASN][1000 genomes]
rs4555592	0.85[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4693981	0.80[ASN][1000 genomes]
rs6815703	0.82[ASN][1000 genomes]
rs6819725	0.83[ASN][1000 genomes]
rs6827857	0.83[ASN][1000 genomes]
rs6834787	0.83[ASN][1000 genomes]
rs6844655	0.83[ASN][1000 genomes]
rs6847562	0.85[AMR][1000 genomes]
rs6852947	0.81[ASN][1000 genomes]
rs7660885	0.81[CEU][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7686954	0.82[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.83[ASN][1000 genomes]
rs7692455	0.83[ASN][1000 genomes]
rs7697075	0.82[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.83[ASN][1000 genomes]
rs7697900	0.82[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.83[ASN][1000 genomes]
rs7697921	0.83[ASN][1000 genomes]
rs8180279	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9307053	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs9307054	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs9307055	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs9307059	0.85[CEU][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9307060	0.83[ASN][1000 genomes]
rs9991237	0.81[JPT][hapmap]
rs9996470	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]

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	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	nsv879532	chr4:89811195-89917135	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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
6	nsv879533	chr4:89832532-89917135	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking 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
7	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
8	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
9	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
10	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
rs6835979	FAM13A	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89878400-89927600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:89879600-89913000	Weak transcription	Aorta	Aorta
3	chr4:89882400-89916400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr4:89894000-89922200	Weak transcription	Fetal Kidney	kidney
5	chr4:89895200-89915400	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:89896800-89934800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:89897400-89913000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:89898600-89914000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr4:89903000-89957200	Weak transcription	HSMM	muscle
10	chr4:89903400-89936000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:89904200-89918200	Weak transcription	Fetal Intestine Large	intestine
12	chr4:89904200-89927600	Weak transcription	Pancreas	Pancrea
13	chr4:89906600-89913000	Weak transcription	A549	lung
14	chr4:89906600-89927400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:89907800-89927400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:89908400-89926600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:89908800-89927400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr4:89909400-89926400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:89909800-89913000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:89909800-89931200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:89910400-89927600	Weak transcription	Ovary	ovary
22	chr4:89910600-89918800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr4:89910800-89913000	Weak transcription	Placenta	Placenta
24	chr4:89910800-89913400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:89910800-89915000	Weak transcription	Fetal Intestine Small	intestine
26	chr4:89910800-89922000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:89910800-89923400	Weak transcription	Fetal Stomach	stomach
28	chr4:89911200-89913400	Enhancers	Osteobl	bone
29	chr4:89911400-89930400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr4:89911600-89913000	Weak transcription	K562	blood
31	chr4:89911600-89913400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:89911600-89915200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr4:89911600-89926400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:89911600-89926600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:89912000-89914600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:89912200-89913200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr4:89912200-89918800	Weak transcription	Fetal Lung	lung
38	chr4:89912200-89921600	Weak transcription	Fetal Brain Male	brain
39	chr4:89912200-89926200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:89912200-89926400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:89912200-89935800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:89912200-89943800	Weak transcription	Psoas Muscle	Psoas
43	chr4:89912400-89913400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:89912400-89913400	Enhancers	HMEC	breast
45	chr4:89912400-89913600	Enhancers	HUVEC	blood vessel
46	chr4:89912400-89914000	Weak transcription	Fetal Heart	heart
47	chr4:89912400-89923200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr4:89912400-89927600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:89912800-89913400	Enhancers	NHEK	skin
50	chr4:89912800-89913600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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