Variant report

Variant	rs10978767
Chromosome Location	chr9:110005698-110005699
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:110004629..110007184-chr9:110036620..110038464,2	MCF-7	breast:
2	chr9:110000595..110013733-chr9:110042800..110048700,27	MCF-7	breast:
3	chr9:110004582..110011651-chr9:110041707..110048879,25	MCF-7	breast:
4	chr9:109999870..110001713-chr9:110004205..110007979,4	K562	blood:
5	chr9:110005542..110008121-chr9:110058915..110061761,2	MCF-7	breast:
6	chr9:109998399..110000270-chr9:110004881..110006442,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10113916	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs10119641	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10481632	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs10521083	0.89[CHB][hapmap];0.84[TSI][hapmap]
rs10732368	0.89[CHB][hapmap]
rs10739232	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs10739234	0.89[CHB][hapmap]
rs10739236	0.83[CHB][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs10739238	0.89[CHB][hapmap]
rs10759218	0.83[CHB][hapmap]
rs10759219	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10759220	0.83[ASN][1000 genomes]
rs10759221	0.83[ASN][1000 genomes]
rs10759222	0.89[CHB][hapmap]
rs10759225	0.84[CHB][hapmap]
rs10816472	0.91[CHD][hapmap];0.81[JPT][hapmap]
rs10816473	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10816474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10816475	0.84[CHB][hapmap]
rs10816477	0.94[CHB][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes]
rs10816480	0.90[AMR][1000 genomes]
rs10816485	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs10816492	0.83[CHB][hapmap]
rs10978764	0.91[CHD][hapmap];0.81[JPT][hapmap]
rs10978766	0.83[ASN][1000 genomes]
rs10978769	1.00[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10978770	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10978775	0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes]
rs10978791	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs12342066	0.93[AMR][1000 genomes]
rs12345455	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap]
rs12555417	0.90[AMR][1000 genomes]
rs1323806	0.84[CHD][hapmap]
rs1323808	0.89[CHB][hapmap]
rs1323809	0.84[CHB][hapmap]
rs1408135	0.84[CHB][hapmap]
rs1519049	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1519050	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1535765	0.89[CHB][hapmap]
rs1535766	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1535767	0.88[ASN][1000 genomes]
rs1805329	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs1805332	0.89[CHB][hapmap]
rs1805334	0.89[CHB][hapmap];0.84[TSI][hapmap]
rs1805335	0.84[CHB][hapmap]
rs1886134	0.89[CHB][hapmap]
rs2147072	0.89[CHB][hapmap]
rs2417784	0.94[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.96[TSI][hapmap]
rs2417785	0.89[CHB][hapmap]
rs2808362	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2808363	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2808365	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28769087	0.90[AMR][1000 genomes]
rs28848858	0.90[AMR][1000 genomes]
rs4278207	0.89[CHB][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]
rs698475	0.94[CHB][hapmap];0.82[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]
rs7038737	0.88[CHB][hapmap]
rs7041137	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs7041497	0.89[CHB][hapmap]
rs7046950	0.89[CHB][hapmap]
rs7847784	0.84[JPT][hapmap]
rs7848194	0.89[CHD][hapmap];0.81[JPT][hapmap]
rs7852259	0.83[ASN][1000 genomes]
rs7852295	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7861304	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7861645	0.81[JPT][hapmap]
rs7862103	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs7866312	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7866353	0.94[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7866797	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7867544	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]
rs7867706	0.81[ASN][1000 genomes]
rs817836	0.94[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs817840	0.94[CHB][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap]
rs817841	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs942291	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap]
rs942292	0.83[CHB][hapmap]
rs942293	0.89[CHB][hapmap]
rs9632893	0.88[CHB][hapmap]
rs9969728	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[MEX][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10978767	TXN	cis	parietal	SCAN

Chromatin state (count:42 , 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	chr9:110001800-110006000	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr9:110002000-110010000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:110002000-110011400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr9:110002400-110006000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:110002400-110006000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr9:110002400-110011000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:110002400-110011200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:110002800-110010200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr9:110003400-110010400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:110003600-110010800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr9:110003800-110006000	Weak transcription	NHLF	lung
14	chr9:110004000-110006400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:110004200-110005800	Weak transcription	Psoas Muscle	Psoas
16	chr9:110004200-110008000	Weak transcription	Fetal Kidney	kidney
17	chr9:110004200-110011200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:110004600-110006600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr9:110004800-110006400	Enhancers	HSMM	muscle
20	chr9:110004800-110006600	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr9:110004800-110006800	Enhancers	Hela-S3	cervix
22	chr9:110004800-110007200	Enhancers	HMEC	breast
23	chr9:110004800-110007200	Enhancers	NHEK	skin
24	chr9:110005000-110006000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:110005000-110006000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:110005000-110006200	Enhancers	Placenta	Placenta
27	chr9:110005000-110006400	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr9:110005000-110006400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:110005000-110006600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:110005000-110006600	Enhancers	NH-A	brain
31	chr9:110005000-110007000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr9:110005200-110005800	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr9:110005200-110005800	Weak transcription	Osteobl	bone
34	chr9:110005200-110006000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:110005200-110006000	Enhancers	A549	lung
36	chr9:110005200-110006400	Enhancers	NHDF-Ad	bronchial
37	chr9:110005400-110005800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr9:110005400-110006200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:110005400-110010000	Weak transcription	HSMMtube	muscle
40	chr9:110005600-110006600	Enhancers	Fetal Intestine Large	intestine
41	chr9:110005600-110006800	Enhancers	Placenta Amnion	Placenta Amnion
42	chr9:110005600-110006800	Enhancers	HepG2	liver

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