Variant report

Variant	rs10490908
Chromosome Location	chr10:116616162-116616163
allele	A/G
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	GATA3	chr10:116615487-116617287	SK-N-SH	brain:	n/a	n/a
2	FOS	chr10:116616113-116616764	MCF10A-Er-Src	breast:	n/a	chr10:116616546-116616557
3	TEAD4	chr10:116616155-116616815	SK-N-SH	brain:	n/a	n/a
4	JUND	chr10:116616103-116616750	Hela-S3	cervix:	n/a	n/a
5	MYC	chr10:116616018-116616579	MCF10A-Er-Src	breast:	n/a	n/a
6	BACH1	chr10:116616079-116616224	H1-hESC	embryonic stem cell:	n/a	n/a
7	TEAD4	chr10:116616146-116616895	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr10:116615602-116616611	IMR90	lung:	n/a	n/a
9	MYC	chr10:116616062-116616262	MCF10A-Er-Src	breast:	n/a	n/a
10	JUND	chr10:116616057-116616845	SK-N-SH	brain:	n/a	n/a
11	NFIC	chr10:116616122-116616898	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr10:116616108-116616857	A549	lung:	n/a	n/a
13	FOS	chr10:116615591-116616752	MCF10A-Er-Src	breast:	n/a	chr10:116616546-116616557 chr10:116615706-116615715
14	MAX	chr10:116616066-116616253	A549	lung:	n/a	n/a
15	EP300	chr10:116616123-116616919	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116611040..116612885-chr10:116615374..116616908,2	K562	blood:

Variant related genes	Relation type
FAM160B1	TF binding region

Extended variants
information (count: 127 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10444099	1.00[JPT][hapmap]
rs1045657	1.00[JPT][hapmap]
rs1046492	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490909	0.82[YRI][hapmap]
rs10510007	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10885613	0.89[AFR][1000 genomes]
rs10885614	0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs10885633	1.00[JPT][hapmap]
rs10885634	1.00[JPT][hapmap]
rs10885636	1.00[JPT][hapmap]
rs10885638	1.00[JPT][hapmap]
rs10885639	1.00[JPT][hapmap]
rs11196929	0.83[AFR][1000 genomes]
rs11196930	0.89[AFR][1000 genomes]
rs11196932	0.89[AFR][1000 genomes]
rs11196935	0.84[AFR][1000 genomes]
rs11196936	0.89[AFR][1000 genomes]
rs11196937	0.89[AFR][1000 genomes]
rs11196939	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs11196941	0.87[AFR][1000 genomes]
rs11196943	0.86[AFR][1000 genomes]
rs11196944	0.88[AFR][1000 genomes]
rs11196945	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs11196947	0.81[AFR][1000 genomes]
rs11196948	0.85[AFR][1000 genomes]
rs11196950	0.85[AFR][1000 genomes]
rs11196951	0.85[AFR][1000 genomes]
rs11196952	0.87[AFR][1000 genomes]
rs11196953	0.87[AFR][1000 genomes]
rs11196963	1.00[CHB][hapmap]
rs11196984	1.00[JPT][hapmap]
rs11196996	1.00[JPT][hapmap]
rs11196999	1.00[JPT][hapmap]
rs11197000	1.00[JPT][hapmap]
rs11197007	1.00[JPT][hapmap]
rs11197010	1.00[JPT][hapmap]
rs11197012	1.00[JPT][hapmap]
rs11818115	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12098332	1.00[JPT][hapmap]
rs12218498	0.88[AFR][1000 genomes]
rs12265048	1.00[JPT][hapmap]
rs12269261	1.00[JPT][hapmap]
rs12415173	0.92[AFR][1000 genomes]
rs12761122	1.00[JPT][hapmap]
rs12764662	1.00[JPT][hapmap]
rs12765350	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12771956	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12772800	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12773943	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12775180	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359079	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs17092497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17586888	0.83[AFR][1000 genomes]
rs17663670	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs17721283	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721905	1.00[JPT][hapmap]
rs17794346	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795212	1.00[JPT][hapmap]
rs1966384	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105001	1.00[JPT][hapmap]
rs2146805	0.86[AFR][1000 genomes]
rs2146806	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420065	0.89[AFR][1000 genomes]
rs2420066	0.89[AFR][1000 genomes]
rs2420067	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs2420069	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs3180654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34064819	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34187191	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34683721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35010779	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35622181	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35628210	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36036948	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089581	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758603	0.87[AFR][1000 genomes]
rs41284358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55711292	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58587374	0.86[AFR][1000 genomes]
rs60820172	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61596353	0.85[AFR][1000 genomes]
rs61867965	0.88[AFR][1000 genomes]
rs61867966	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61867967	1.00[ASN][1000 genomes]
rs61868018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6585309	1.00[JPT][hapmap]
rs6585310	1.00[JPT][hapmap]
rs6585311	1.00[JPT][hapmap]
rs68085797	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071789	1.00[JPT][hapmap]
rs7071812	1.00[JPT][hapmap]
rs7072356	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072364	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7074729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7075888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7079877	0.87[AFR][1000 genomes]
rs7089973	0.83[CEU][hapmap]
rs7093674	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094072	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099565	1.00[JPT][hapmap]
rs7099590	1.00[JPT][hapmap]
rs7100026	1.00[JPT][hapmap]
rs749649	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897937	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs7898249	1.00[JPT][hapmap]
rs7903663	0.87[AFR][1000 genomes]
rs7904188	0.92[AFR][1000 genomes]
rs7904605	1.00[JPT][hapmap]
rs7908069	1.00[JPT][hapmap]
rs7908464	1.00[JPT][hapmap]
rs7909566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7914792	0.89[AFR][1000 genomes]
rs7918253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7919649	0.92[AFR][1000 genomes]
rs7920216	0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs7923295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181444	0.89[AFR][1000 genomes]
rs881192	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv831996	chr10:116601552-116772968	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10490908	FAM160B1	cis	Adipose Subcutaneous	GTEx
rs10490908	DCP1A	cis	Brain Pons	GTEx
rs10490908	TRUB1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116583000-116617600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:116583200-116616800	Weak transcription	K562	blood
3	chr10:116589600-116626600	Weak transcription	Stomach Mucosa	stomach
4	chr10:116589600-116640600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:116590800-116616600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr10:116590800-116624400	Strong transcription	Dnd41	blood
7	chr10:116590800-116625600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr10:116590800-116626400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr10:116591000-116619400	Strong transcription	Fetal Muscle Leg	muscle
10	chr10:116591000-116624800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr10:116591000-116626600	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr10:116592400-116625200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr10:116592600-116616600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr10:116593000-116616800	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr10:116595800-116623000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr10:116596000-116617000	Strong transcription	Adipose Nuclei	Adipose
17	chr10:116602600-116624800	Strong transcription	Duodenum Mucosa	Duodenum
18	chr10:116604800-116627200	Weak transcription	Small Intestine	intestine
19	chr10:116606200-116624200	Weak transcription	Gastric	stomach
20	chr10:116606600-116619800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr10:116609200-116619000	Weak transcription	Right Ventricle	heart
22	chr10:116609400-116623400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr10:116609600-116619000	Weak transcription	Aorta	Aorta
24	chr10:116609600-116634800	Weak transcription	Spleen	Spleen
25	chr10:116609600-116639400	Weak transcription	Pancreas	Pancrea
26	chr10:116609800-116616600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr10:116610200-116625000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr10:116610200-116625000	Weak transcription	Colonic Mucosa	Colon
29	chr10:116610200-116625400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr10:116610200-116625600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr10:116610200-116634600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr10:116610400-116617600	Weak transcription	Fetal Brain Male	brain
33	chr10:116610400-116617600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr10:116610400-116628000	Weak transcription	Esophagus	oesophagus
35	chr10:116610600-116628000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr10:116610800-116616600	Weak transcription	Fetal Stomach	stomach
37	chr10:116610800-116619000	Weak transcription	Brain Germinal Matrix	brain
38	chr10:116610800-116619000	Weak transcription	Ovary	ovary
39	chr10:116611000-116616600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr10:116611000-116619000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr10:116611400-116624600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr10:116611600-116641000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr10:116611800-116617200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr10:116612400-116619000	Weak transcription	Lung	lung
45	chr10:116612400-116619000	Weak transcription	Thymus	Thymus
46	chr10:116612400-116625800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr10:116612800-116619000	Weak transcription	Psoas Muscle	Psoas
48	chr10:116612800-116625600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr10:116612800-116626600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr10:116613600-116625400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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