Variant report

Variant	rs7867544
Chromosome Location	chr9:110013980-110013981
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:110012891..110014822-chr9:110023736..110026167,2	MCF-7	breast:
2	chr9:110009648..110012591-chr9:110013011..110015349,2	K562	blood:
3	chr9:110007276..110009572-chr9:110012956..110014515,2	K562	blood:
4	chr9:110009341..110011173-chr9:110013824..110016663,3	MCF-7	breast:
5	chr9:110011669..110017049-chr9:110043880..110047775,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10113916	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs10119641	0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs10122970	0.81[ASN][1000 genomes]
rs10481632	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs10521083	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[TSI][hapmap]
rs10732368	0.89[CHB][hapmap]
rs10739232	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs10739234	0.89[CHB][hapmap]
rs10739236	0.83[CHB][hapmap];0.91[CHD][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs10739238	0.89[CHB][hapmap]
rs10759218	0.83[CHB][hapmap]
rs10759219	0.94[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10759220	0.81[ASN][1000 genomes]
rs10759221	0.81[ASN][1000 genomes]
rs10759222	0.89[CHB][hapmap];0.88[CHD][hapmap]
rs10759225	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs10816472	0.81[JPT][hapmap]
rs10816473	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10816474	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10816475	0.84[CHB][hapmap]
rs10816477	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]
rs10816480	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10816485	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs10816492	0.83[CHB][hapmap]
rs10978764	0.81[JPT][hapmap]
rs10978766	0.81[ASN][1000 genomes]
rs10978767	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10978769	0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[ASN][1000 genomes]
rs10978770	0.94[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10978775	0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10978776	0.81[ASN][1000 genomes]
rs10978777	0.81[ASN][1000 genomes]
rs10978791	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs12342066	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12345455	0.94[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.81[ASN][1000 genomes]
rs12555417	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1323808	0.89[CHB][hapmap]
rs1323809	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs1408135	0.84[CHB][hapmap]
rs1519049	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1519050	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1535765	0.89[CHB][hapmap]
rs1535766	0.94[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs1535767	0.86[ASN][1000 genomes]
rs1805329	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs1805332	0.89[CHB][hapmap];0.91[CHD][hapmap]
rs1805334	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[TSI][hapmap]
rs1805335	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs1886134	0.89[CHB][hapmap]
rs2005143	0.80[ASN][1000 genomes]
rs2147072	0.89[CHB][hapmap];0.88[CHD][hapmap]
rs2417776	0.81[ASN][1000 genomes]
rs2417784	0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.96[TSI][hapmap]
rs2417785	0.89[CHB][hapmap]
rs2808362	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2808363	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2808365	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28769087	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28848858	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4278207	0.89[CHB][hapmap];0.91[CHD][hapmap];0.80[TSI][hapmap]
rs4481670	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs4978764	0.84[CHB][hapmap]
rs4978849	0.89[CHB][hapmap]
rs61701375	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs698475	0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs7029997	0.89[CHB][hapmap]
rs7030169	0.89[CHB][hapmap]
rs7031906	0.89[CHB][hapmap]
rs7035611	0.89[CHB][hapmap];0.91[CHD][hapmap]
rs7036284	0.81[ASN][1000 genomes]
rs7038737	0.88[CHB][hapmap]
rs7041137	0.94[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap]
rs7041497	0.89[CHB][hapmap];0.91[CHD][hapmap]
rs7046950	0.89[CHB][hapmap]
rs7847784	0.84[JPT][hapmap]
rs7848194	0.81[JPT][hapmap]
rs7852259	0.81[ASN][1000 genomes]
rs7852295	0.94[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7861304	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7861645	0.81[JPT][hapmap]
rs7862103	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs7866312	0.94[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7866353	0.94[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7866797	0.94[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7873745	0.80[ASN][1000 genomes]
rs817836	0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs817840	0.94[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap]
rs817841	0.94[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]
rs942291	0.94[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.81[ASN][1000 genomes]
rs942292	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs942293	0.89[CHB][hapmap]
rs9632893	0.88[CHB][hapmap]
rs9969728	0.94[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.81[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
rs7867544	OR13C8	cis	cerebellum	SCAN
rs7867544	TXN	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110007000-110022600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:110008800-110014200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:110008800-110014400	Weak transcription	Fetal Kidney	kidney
4	chr9:110009800-110015400	Enhancers	Fetal Muscle Leg	muscle
5	chr9:110010000-110014200	Enhancers	HSMMtube	muscle
6	chr9:110011200-110014200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:110011400-110014600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr9:110011800-110014200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:110012000-110014200	Enhancers	HepG2	liver
10	chr9:110012200-110014000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:110012200-110014200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:110012400-110014000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:110012400-110014200	Weak transcription	Liver	Liver
14	chr9:110012400-110014200	Weak transcription	A549	lung
15	chr9:110012400-110014400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:110012400-110014400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr9:110012400-110022600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:110013000-110014200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:110013000-110014400	Enhancers	NHLF	lung
20	chr9:110013200-110014600	Enhancers	Fetal Lung	lung
21	chr9:110013200-110015000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:110013400-110014200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:110013400-110015000	Enhancers	HSMM	muscle
24	chr9:110013400-110015400	Enhancers	Placenta	Placenta
25	chr9:110013600-110014000	Enhancers	Aorta	Aorta
26	chr9:110013600-110014200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:110013600-110014200	Enhancers	Pancreas	Pancrea
28	chr9:110013600-110014200	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr9:110013600-110014200	Enhancers	NH-A	brain
30	chr9:110013600-110014200	Enhancers	Osteobl	bone
31	chr9:110013600-110014400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:110013600-110014600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr9:110013600-110014600	Enhancers	Left Ventricle	heart
34	chr9:110013600-110014600	Enhancers	Ovary	ovary
35	chr9:110013600-110014600	Enhancers	Psoas Muscle	Psoas
36	chr9:110013600-110014800	Enhancers	HMEC	breast
37	chr9:110013600-110015000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr9:110013600-110015000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr9:110013600-110015000	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr9:110013600-110015400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:110013800-110014000	Flanking Active TSS	NHDF-Ad	bronchial
42	chr9:110013800-110014200	Enhancers	Fetal Heart	heart
43	chr9:110013800-110014600	Enhancers	NHEK	skin
44	chr9:110013800-110014800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr9:110013800-110014800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr9:110013800-110014800	Enhancers	Adipose Nuclei	Adipose
47	chr9:110013800-110014800	Enhancers	Colon Smooth Muscle	Colon
48	chr9:110013800-110014800	Enhancers	Rectal Smooth Muscle	rectum
49	chr9:110013800-110014800	Enhancers	K562	blood

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