Variant report

Variant	rs10816477
Chromosome Location	chr9:110022842-110022843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:110021248..110023658-chr9:110046181..110048340,2	K562	blood:
2	chr9:110021549..110024530-chr9:110031690..110034147,2	MCF-7	breast:
3	chr9:110022591..110024814-chr9:110044876..110048033,4	MCF-7	breast:
4	chr9:110022816..110024667-chr9:110034684..110036365,2	MCF-7	breast:
5	chr9:110022283..110024488-chr9:110040936..110043082,2	MCF-7	breast:
6	chr9:110007992..110013194-chr9:110021107..110025881,5	MCF-7	breast:
7	chr9:110021032..110023010-chr9:110046369..110047881,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

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

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

rs_ID	r²[population]
rs10113916	1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10119641	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs10122970	1.00[ASN][1000 genomes]
rs10481632	1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10521083	0.84[CHB][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.85[AFR][1000 genomes]
rs10732368	0.84[CHB][hapmap]
rs10739232	0.87[CHB][hapmap]
rs10739234	0.84[CHB][hapmap];0.85[AFR][1000 genomes]
rs10739236	1.00[ASW][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10739238	0.84[CHB][hapmap];0.85[AFR][1000 genomes]
rs10759219	0.89[CHB][hapmap]
rs10759222	0.84[CHB][hapmap]
rs10816473	0.84[AMR][1000 genomes]
rs10816474	0.97[AMR][1000 genomes]
rs10816480	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10816485	1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10816490	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10816491	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10978767	0.94[CHB][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes]
rs10978769	0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap]
rs10978770	0.89[CHB][hapmap]
rs10978775	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978776	1.00[ASN][1000 genomes]
rs10978777	1.00[ASN][1000 genomes]
rs10978791	1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12342066	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345455	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs12555417	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323808	0.84[CHB][hapmap]
rs1519049	0.86[AMR][1000 genomes]
rs1519050	0.89[AMR][1000 genomes]
rs1535765	0.84[CHB][hapmap]
rs1535766	0.89[CHB][hapmap]
rs1805329	1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1805332	0.84[CHB][hapmap]
rs1805334	0.84[CHB][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap]
rs1886134	0.84[CHB][hapmap];0.85[AFR][1000 genomes]
rs2005143	0.95[ASN][1000 genomes]
rs2147072	0.84[CHB][hapmap]
rs2417776	1.00[ASN][1000 genomes]
rs2417784	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2417785	0.84[CHB][hapmap]
rs2808362	0.89[AMR][1000 genomes]
rs2808363	0.89[AMR][1000 genomes]
rs2808365	0.89[AMR][1000 genomes]
rs28534368	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28769087	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28848858	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4278207	0.84[CHB][hapmap];0.89[MKK][hapmap];0.80[TSI][hapmap];0.85[AFR][1000 genomes]
rs4481670	0.82[CHB][hapmap]
rs4978404	0.85[AFR][1000 genomes]
rs4978406	0.85[AFR][1000 genomes]
rs4978849	0.83[CHB][hapmap];0.85[AFR][1000 genomes]
rs61701375	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs698475	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7029997	0.84[CHB][hapmap]
rs7030169	0.84[CHB][hapmap]
rs7031906	0.84[CHB][hapmap]
rs7035611	0.84[CHB][hapmap];0.89[MKK][hapmap];0.85[AFR][1000 genomes]
rs7036284	1.00[ASN][1000 genomes]
rs7038737	0.83[CHB][hapmap];0.85[AFR][1000 genomes]
rs7039041	0.85[AFR][1000 genomes]
rs7040217	0.92[ASN][1000 genomes]
rs7041137	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs7041497	0.84[CHB][hapmap];0.85[AFR][1000 genomes]
rs7046950	0.84[CHB][hapmap]
rs7852295	0.89[CHB][hapmap]
rs7856227	0.85[AFR][1000 genomes]
rs7861304	0.87[AMR][1000 genomes]
rs7866312	0.89[CHB][hapmap]
rs7866353	0.89[CHB][hapmap]
rs7866797	0.89[CHB][hapmap]
rs7867544	0.94[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7873745	0.99[ASN][1000 genomes]
rs817836	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817838	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs817839	0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs817840	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs817841	1.00[ASW][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.89[MKK][hapmap];0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs817843	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs817844	0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs817845	0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs817847	0.81[ASN][1000 genomes]
rs942291	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs942293	0.84[CHB][hapmap];0.85[AFR][1000 genomes]
rs9632893	0.94[CHB][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9969728	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];1.00[ASN][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	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831682	chr9:109937181-110075453	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893698	chr9:109998563-110052660	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv508560	chr9:110006490-110060539	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10816477	OR13C8	cis	cerebellum	SCAN
rs10816477	TXN	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110021000-110023800	Enhancers	Liver	Liver
2	chr9:110021400-110024000	Enhancers	Primary B cells from peripheral blood	blood
3	chr9:110022200-110023800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:110022400-110023200	Enhancers	NHLF	lung
5	chr9:110022400-110024000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:110022600-110023000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr9:110022600-110023000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr9:110022600-110023200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:110022600-110023200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:110022600-110023200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:110022600-110023400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:110022600-110023400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:110022600-110023400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:110022600-110023400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:110022600-110023400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr9:110022600-110023400	Enhancers	A549	lung
17	chr9:110022600-110023400	Flanking Active TSS	HepG2	liver
18	chr9:110022600-110023400	Enhancers	HMEC	breast
19	chr9:110022600-110023400	Enhancers	NHEK	skin
20	chr9:110022600-110023600	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr9:110022600-110023600	Flanking Active TSS	GM12878-XiMat	blood
22	chr9:110022600-110023800	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr9:110022600-110023800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:110022600-110023800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:110022600-110023800	Enhancers	Adipose Nuclei	Adipose
26	chr9:110022600-110023800	Enhancers	Fetal Kidney	kidney
27	chr9:110022600-110023800	Enhancers	Placenta	Placenta
28	chr9:110022600-110023800	Enhancers	HSMM	muscle
29	chr9:110022600-110023800	Enhancers	HSMMtube	muscle
30	chr9:110022600-110023800	Enhancers	Osteobl	bone
31	chr9:110022600-110024000	Enhancers	NHDF-Ad	bronchial
32	chr9:110022800-110023200	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr9:110022800-110023200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:110022800-110023400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:110022800-110023600	Enhancers	HUES64 Cell Line	embryonic stem cell

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