Variant report

Variant	rs10277362
Chromosome Location	chr7:98993112-98993113
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:98992027..98994559-chr7:99000326..99002906,3	MCF-7	breast:
2	chr7:98988826..98993566-chr7:99002963..99006762,7	MCF-7	breast:
3	chr7:98970545..98974719-chr7:98992685..98998543,7	MCF-7	breast:
4	chr7:98971244..98973231-chr7:98989224..98993180,5	MCF-7	breast:
5	chr7:98983107..98985699-chr7:98992878..98994475,2	MCF-7	breast:
6	chr7:98966757..98974253-chr7:98988800..98995304,7	K562	blood:

Variant related genes	Relation type
ENSG00000130429	Chromatin interaction
ENSG00000106245	Chromatin interaction
ENSG00000106244	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10085823	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10155956	0.86[AMR][1000 genomes]
rs10231948	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10237212	1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs10239443	0.86[EUR][1000 genomes]
rs10247946	1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs10249659	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10263954	0.86[AMR][1000 genomes]
rs10264303	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10271695	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12386578	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13438585	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs14935	1.00[CEU][hapmap]
rs17161650	1.00[MEX][hapmap]
rs28378107	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28497153	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28564953	0.86[EUR][1000 genomes]
rs28655791	1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs28754375	0.86[AMR][1000 genomes]
rs3197990	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45529834	1.00[EUR][1000 genomes]
rs45558438	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45599236	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45610838	1.00[EUR][1000 genomes]
rs59463042	0.82[AMR][1000 genomes]
rs60971917	0.82[AMR][1000 genomes]
rs60996680	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61435529	0.86[EUR][1000 genomes]
rs755145	1.00[MEX][hapmap]
rs940334	1.00[CEU][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv971208	chr7:98992671-98997201	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10277362	ATP5J2	cis	lymphoblastoid	seeQTL
rs10277362	STAG3	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98979400-99001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:98980400-99003800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr7:98980800-99000600	Strong transcription	Dnd41	blood
4	chr7:98985600-99003800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:98987000-99004200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:98990000-99002800	Strong transcription	GM12878-XiMat	blood
7	chr7:98990200-98994600	Weak transcription	NHDF-Ad	bronchial
8	chr7:98991000-98993200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr7:98991000-98995000	Weak transcription	Aorta	Aorta
10	chr7:98991000-98996200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr7:98991000-99001600	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr7:98991000-99001600	Strong transcription	Osteobl	bone
13	chr7:98991000-99002000	Strong transcription	NHEK	skin
14	chr7:98991000-99002600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr7:98991000-99002600	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr7:98991200-98993800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr7:98991200-98996400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:98991200-98996600	Strong transcription	HSMM	muscle
19	chr7:98991400-98993600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr7:98991400-98994200	Weak transcription	Ovary	ovary
21	chr7:98991400-98995400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr7:98991400-99001800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr7:98991400-99001800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr7:98991400-99001800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr7:98991400-99002400	Strong transcription	Esophagus	oesophagus
26	chr7:98991400-99002400	Weak transcription	Right Atrium	heart
27	chr7:98991400-99004200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr7:98991600-98993200	Weak transcription	Brain Angular Gyrus	brain
29	chr7:98991600-98993200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr7:98991600-98993400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr7:98991600-98993800	Strong transcription	Rectal Smooth Muscle	rectum
32	chr7:98991600-98994600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr7:98991600-98995400	Strong transcription	NH-A	brain
34	chr7:98991600-98996200	Strong transcription	HMEC	breast
35	chr7:98991600-98996400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr7:98991600-98997200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr7:98991600-98999000	Strong transcription	Primary B cells from cord blood	blood
38	chr7:98991600-99001400	Strong transcription	Placenta	Placenta
39	chr7:98991600-99001600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr7:98991600-99001800	Strong transcription	NHLF	lung
41	chr7:98991600-99002000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr7:98991600-99002000	Strong transcription	Adipose Nuclei	Adipose
43	chr7:98991600-99002400	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr7:98991600-99002800	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:98991600-99003000	Strong transcription	Primary T cells from cord blood	blood
46	chr7:98991600-99003000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr7:98991600-99003400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr7:98991600-99003400	Weak transcription	Stomach Mucosa	stomach
49	chr7:98991600-99003400	Strong transcription	K562	blood
50	chr7:98991600-99005200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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