Variant report

Variant	rs10258465
Chromosome Location	chr7:140408569-140408570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10228254	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10230071	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10230163	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10258462	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1140034	0.85[ASN][1000 genomes]
rs2364395	0.85[ASN][1000 genomes]
rs2364396	0.83[ASN][1000 genomes]
rs2364397	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28533681	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2907949	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2907950	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2930315	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2930318	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2930319	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968548	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2968549	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2968550	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2968551	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2968553	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968555	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2968558	0.85[ASN][1000 genomes]
rs2968559	0.85[ASN][1000 genomes]
rs4624945	0.85[ASN][1000 genomes]
rs4727011	0.85[ASN][1000 genomes]
rs4727072	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6464937	0.85[ASN][1000 genomes]
rs6464984	0.83[ASN][1000 genomes]
rs6949396	0.81[ASN][1000 genomes]
rs6953568	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6962426	0.83[ASN][1000 genomes]
rs6977834	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73489531	0.83[ASN][1000 genomes]
rs7803697	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][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	nsv831157	chr7:140241339-140426876	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv3351231	chr7:140390303-140588539	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv831158	chr7:140392222-140602315	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv869260	chr7:140404835-140542905	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10258465	NDUFB2	Cis_1M	lymphoblastoid	RTeQTL
rs10258465	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140398000-140408800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr7:140398000-140419400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr7:140398000-140466600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:140398200-140473800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr7:140398200-140492600	Weak transcription	Colonic Mucosa	Colon
6	chr7:140398400-140422000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr7:140398400-140432200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:140398600-140414800	Weak transcription	Small Intestine	intestine
9	chr7:140398600-140459400	Weak transcription	Brain Germinal Matrix	brain
10	chr7:140398600-140491800	Weak transcription	Fetal Brain Male	brain
11	chr7:140399400-140414200	Weak transcription	Gastric	stomach
12	chr7:140399400-140468200	Weak transcription	Right Ventricle	heart
13	chr7:140399600-140443800	Weak transcription	Fetal Heart	heart
14	chr7:140400000-140474000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr7:140404400-140452400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr7:140404800-140414200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr7:140404800-140419600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr7:140404800-140427600	Weak transcription	HSMMtube	muscle
19	chr7:140404800-140489000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:140404800-140517000	Weak transcription	Psoas Muscle	Psoas
21	chr7:140405200-140470800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr7:140405600-140472200	Weak transcription	Brain Substantia Nigra	brain
23	chr7:140406000-140414200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr7:140406200-140418800	Weak transcription	Fetal Kidney	kidney
25	chr7:140406400-140408800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:140406400-140409200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr7:140406600-140414000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:140406600-140472800	Weak transcription	Hela-S3	cervix
29	chr7:140407000-140413800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:140407000-140414200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr7:140407000-140425600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:140407000-140425600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:140407000-140427400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr7:140407000-140427600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr7:140407000-140428800	Weak transcription	NHLF	lung
36	chr7:140407000-140454200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr7:140407000-140466800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr7:140407200-140409000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr7:140407200-140409400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr7:140407200-140409600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr7:140407200-140409600	Weak transcription	Brain Angular Gyrus	brain
42	chr7:140407200-140410000	Weak transcription	Colon Smooth Muscle	Colon
43	chr7:140407200-140412400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr7:140407200-140413600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr7:140407200-140413800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr7:140407200-140413800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr7:140407200-140413800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr7:140407200-140413800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr7:140407200-140413800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr7:140407200-140413800	Weak transcription	Primary T cells fromperipheralblood	blood

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