Variant report

Variant	rs1046492
Chromosome Location	chr10:116624067-116624068
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116601872..116604091-chr10:116621422..116624270,3	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10490908	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[ASW][hapmap]
rs10510007	0.92[CEU][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10885613	0.89[AFR][1000 genomes]
rs10885614	0.92[YRI][hapmap];0.92[AFR][1000 genomes]
rs11196924	0.90[ASW][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	1.00[ASW][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.92[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	0.92[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]
rs11818115	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12218498	0.88[AFR][1000 genomes]
rs12415173	0.92[AFR][1000 genomes]
rs12765350	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12771956	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12772800	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12773943	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12775180	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359079	1.00[ASW][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs17092497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092542	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17586888	0.83[AFR][1000 genomes]
rs17663670	1.00[ASW][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs17721283	0.92[CEU][hapmap];0.81[GIH][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17794346	0.92[CEU][hapmap];0.81[GIH][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1966384	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146805	0.86[AFR][1000 genomes]
rs2146806	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420065	0.89[AFR][1000 genomes]
rs2420066	0.89[AFR][1000 genomes]
rs2420067	1.00[ASW][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs2420069	1.00[ASW][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs3180654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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];0.80[EUR][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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35622181	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35628210	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36036948	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089581	0.86[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55711292	0.85[AMR][1000 genomes];0.84[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61596353	0.85[AFR][1000 genomes]
rs61867965	0.88[AFR][1000 genomes]
rs61867966	0.85[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68085797	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072356	0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7075888	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094072	0.96[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749649	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895551	1.00[CEU][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897937	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs7903663	0.87[AFR][1000 genomes]
rs7904188	0.92[AFR][1000 genomes]
rs7909566	1.00[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909657	1.00[CEU][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181444	0.89[AFR][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1046492	DCP1A	cis	Brain Pons	GTEx
rs1046492	FAM160B1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116589600-116626600	Weak transcription	Stomach Mucosa	stomach
2	chr10:116589600-116640600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:116590800-116624400	Strong transcription	Dnd41	blood
4	chr10:116590800-116625600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr10:116590800-116626400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr10:116591000-116624800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr10:116591000-116626600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr10:116592400-116625200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr10:116602600-116624800	Strong transcription	Duodenum Mucosa	Duodenum
10	chr10:116604800-116627200	Weak transcription	Small Intestine	intestine
11	chr10:116606200-116624200	Weak transcription	Gastric	stomach
12	chr10:116609600-116634800	Weak transcription	Spleen	Spleen
13	chr10:116609600-116639400	Weak transcription	Pancreas	Pancrea
14	chr10:116610200-116625000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr10:116610200-116625000	Weak transcription	Colonic Mucosa	Colon
16	chr10:116610200-116625400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:116610200-116625600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr10:116610200-116634600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr10:116610400-116628000	Weak transcription	Esophagus	oesophagus
20	chr10:116610600-116628000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr10:116611400-116624600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr10:116611600-116641000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr10:116612400-116625800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr10:116612800-116625600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr10:116612800-116626600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr10:116613600-116625400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr10:116614000-116625000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr10:116614000-116626200	Strong transcription	Primary hematopoietic stem cells	blood
29	chr10:116614400-116624400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr10:116614400-116624600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr10:116614400-116624800	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr10:116614400-116626200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr10:116614800-116628400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr10:116616200-116624400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr10:116616800-116624400	Weak transcription	Brain Angular Gyrus	brain
36	chr10:116616800-116624400	Weak transcription	Fetal Heart	heart
37	chr10:116616800-116625400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr10:116616800-116625400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr10:116616800-116626400	Weak transcription	Brain Substantia Nigra	brain
40	chr10:116617000-116627400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr10:116617000-116630200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr10:116617400-116624800	Strong transcription	Placenta	Placenta
43	chr10:116617400-116640600	Weak transcription	Fetal Intestine Small	intestine
44	chr10:116617600-116624400	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr10:116617600-116624400	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr10:116617600-116625600	Strong transcription	Adipose Nuclei	Adipose
47	chr10:116617800-116626000	Strong transcription	HSMM	muscle
48	chr10:116617800-116626400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr10:116618000-116624600	Strong transcription	NH-A	brain
50	chr10:116618000-116626400	Strong transcription	Muscle Satellite Cultured Cells	--

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