Variant report

Variant	rs7866797
Chromosome Location	chr9:110003509-110003510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:110000595..110013733-chr9:110042800..110048700,27	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10113916	0.89[CHB][hapmap]
rs10119641	0.89[CHB][hapmap]
rs10481632	0.89[CHB][hapmap]
rs10521083	0.83[CHB][hapmap]
rs10732368	0.83[CHB][hapmap]
rs10739232	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739234	0.83[CHB][hapmap]
rs10739238	0.83[CHB][hapmap]
rs10759218	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10759219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759221	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759222	0.83[CHB][hapmap]
rs10759225	0.89[CHB][hapmap]
rs10816471	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10816472	1.00[CEU][hapmap];0.80[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10816473	0.83[ASN][1000 genomes]
rs10816474	0.83[ASN][1000 genomes]
rs10816475	0.89[CHB][hapmap]
rs10816477	0.89[CHB][hapmap]
rs10816485	0.89[CHB][hapmap]
rs10816492	0.89[CHB][hapmap]
rs10978764	1.00[CEU][hapmap];0.80[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10978765	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10978766	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978767	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10978769	0.89[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10978770	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10978775	0.89[CHB][hapmap]
rs10978791	0.89[CHB][hapmap]
rs12345455	0.89[CHB][hapmap]
rs1323806	0.85[CHB][hapmap];0.89[CHD][hapmap]
rs1323808	0.83[CHB][hapmap]
rs1323809	0.89[CHB][hapmap]
rs1408135	0.89[CHB][hapmap]
rs1519051	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1519052	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1535765	0.83[CHB][hapmap]
rs1535766	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs1535767	0.92[ASN][1000 genomes]
rs1805329	0.89[CHB][hapmap]
rs1805332	0.83[CHB][hapmap]
rs1805334	0.83[CHB][hapmap]
rs1886134	0.83[CHB][hapmap]
rs2015605	0.82[ASN][1000 genomes]
rs2147072	0.83[CHB][hapmap]
rs2417784	0.89[CHB][hapmap]
rs2417785	0.83[CHB][hapmap]
rs2680216	0.81[AFR][1000 genomes]
rs2680218	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2680219	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2808364	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4278207	0.83[CHB][hapmap]
rs4481670	0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4978764	0.89[CHB][hapmap]
rs4978849	0.83[CHB][hapmap]
rs698475	0.89[CHB][hapmap]
rs7029997	0.83[CHB][hapmap]
rs7030169	0.83[CHB][hapmap]
rs7031906	0.83[CHB][hapmap]
rs7035611	0.83[CHB][hapmap]
rs7038737	0.82[CHB][hapmap]
rs7041137	0.88[CHB][hapmap]
rs7041497	0.83[CHB][hapmap]
rs7046950	0.83[CHB][hapmap]
rs7847661	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7847784	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7848194	0.80[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7852259	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852295	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7861304	0.83[ASN][1000 genomes]
rs7861645	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7861827	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7862063	1.00[CEU][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7862103	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7866312	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866353	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867544	0.94[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7867706	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7873081	0.95[ASN][1000 genomes]
rs817836	0.89[CHB][hapmap]
rs817840	0.89[CHB][hapmap]
rs817841	0.89[CHB][hapmap]
rs942291	0.89[CHB][hapmap]
rs942293	0.83[CHB][hapmap]
rs9632893	0.83[CHB][hapmap]
rs9969728	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7866797	TXN	cis	parietal	SCAN
rs7866797	TMEM38B	cis	parietal	SCAN
rs7866797	CYLC2	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:109998600-110006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:109999200-110008600	Weak transcription	Liver	Liver
3	chr9:110000800-110003600	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr9:110001800-110006000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr9:110002000-110005000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:110002000-110010000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:110002000-110011400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr9:110002400-110003800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr9:110002400-110005000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:110002400-110005600	Weak transcription	HepG2	liver
11	chr9:110002400-110006000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:110002400-110006000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr9:110002400-110011000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:110002400-110011200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr9:110002800-110010200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr9:110003000-110004000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:110003200-110003600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr9:110003200-110003600	Weak transcription	Placenta	Placenta
19	chr9:110003200-110004200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr9:110003200-110004800	Enhancers	NHDF-Ad	bronchial
21	chr9:110003400-110003600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:110003400-110003600	Enhancers	HMEC	breast
23	chr9:110003400-110003800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:110003400-110003800	Enhancers	NHLF	lung
25	chr9:110003400-110004000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:110003400-110004200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr9:110003400-110004200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:110003400-110004200	Enhancers	Fetal Kidney	kidney
29	chr9:110003400-110010400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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