Variant report

Variant	rs10919149
Chromosome Location	chr1:169333835-169333836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:169333798-169333997	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169331328..169334287-chr1:169334911..169337205,2	MCF-7	breast:
2	chr1:169324847..169326824-chr1:169332989..169335675,2	K562	blood:
3	chr1:169332852..169334456-chr1:169336922..169338977,2	MCF-7	breast:

Variant related genes	Relation type
BLZF1	TF binding region
ENSG00000117475	Chromatin interaction
ENSG00000143156	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10458394	1.00[AFR][1000 genomes]
rs10489190	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489417	1.00[AFR][1000 genomes]
rs10494477	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10494478	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800433	1.00[AFR][1000 genomes]
rs10919122	1.00[AFR][1000 genomes]
rs10919123	1.00[AFR][1000 genomes]
rs10919125	1.00[AFR][1000 genomes]
rs10919127	1.00[AFR][1000 genomes]
rs10919147	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10919150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919153	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919158	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919162	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919165	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919172	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12021696	1.00[AFR][1000 genomes]
rs12022617	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022768	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12025397	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12025721	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028197	1.00[AFR][1000 genomes]
rs12028208	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12029800	1.00[AFR][1000 genomes]
rs12030541	1.00[AFR][1000 genomes]
rs12030810	1.00[AFR][1000 genomes]
rs12031371	1.00[AFR][1000 genomes]
rs12036426	1.00[AFR][1000 genomes]
rs12037926	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12042990	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12044982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045803	1.00[AFR][1000 genomes]
rs12048188	1.00[AFR][1000 genomes]
rs12401962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12401966	1.00[AFR][1000 genomes]
rs12402774	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12405185	1.00[AFR][1000 genomes]
rs12405725	1.00[AFR][1000 genomes]
rs12408636	1.00[AFR][1000 genomes]
rs12410241	1.00[AFR][1000 genomes]
rs12410387	1.00[AFR][1000 genomes]
rs12410456	1.00[AFR][1000 genomes]
rs12567342	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1517742	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1517746	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17345426	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17345531	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17349677	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17518147	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17576927	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1949426	1.00[ASN][1000 genomes]
rs2001156	1.00[AFR][1000 genomes]
rs2092083	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34323371	1.00[AFR][1000 genomes]
rs3766100	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766101	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4497270	1.00[AFR][1000 genomes]
rs4562680	1.00[AFR][1000 genomes]
rs72704035	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72706084	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7414819	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7522565	0.93[ASN][1000 genomes]
rs7546361	0.93[ASN][1000 genomes]
rs7554853	1.00[ASN][1000 genomes]
rs7556463	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10919149	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
3	chr1:169309400-169336400	Weak transcription	Ovary	ovary
4	chr1:169311000-169336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:169316000-169334200	Weak transcription	Fetal Intestine Small	intestine
6	chr1:169317000-169336400	Weak transcription	Pancreas	Pancrea
7	chr1:169317800-169335800	Weak transcription	Fetal Lung	lung
8	chr1:169318200-169334000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:169324600-169335800	Weak transcription	Primary T cells from cord blood	blood
10	chr1:169325600-169335800	Weak transcription	K562	blood
11	chr1:169326200-169334200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:169327200-169335800	Weak transcription	Small Intestine	intestine
13	chr1:169327200-169336200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:169330000-169336400	Weak transcription	Psoas Muscle	Psoas
15	chr1:169330800-169335800	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:169330800-169336400	Weak transcription	Right Ventricle	heart
17	chr1:169331400-169335800	Weak transcription	Fetal Intestine Large	intestine
18	chr1:169331600-169335600	Enhancers	HMEC	breast
19	chr1:169331800-169335800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:169331800-169336200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:169332000-169334400	Enhancers	NHEK	skin
22	chr1:169332000-169335800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:169332200-169334200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:169332200-169336400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:169332800-169334600	Enhancers	Placenta	Placenta
26	chr1:169332800-169334800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:169332800-169336400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr1:169333000-169334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:169333000-169334400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:169333000-169336000	Weak transcription	NHDF-Ad	bronchial
31	chr1:169333000-169336200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:169333000-169336200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:169333000-169336200	Weak transcription	Thymus	Thymus
34	chr1:169333200-169334200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:169333200-169334200	Weak transcription	Dnd41	blood
36	chr1:169333200-169334400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:169333200-169335800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:169333200-169335800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:169333200-169335800	Weak transcription	NHLF	lung
40	chr1:169333200-169336000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:169333200-169336200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr1:169333200-169336200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr1:169333200-169336200	Weak transcription	Fetal Stomach	stomach
44	chr1:169333200-169336200	Enhancers	Hela-S3	cervix
45	chr1:169333200-169336400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:169333200-169336400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:169333400-169335800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:169333400-169335800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:169333400-169335800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:169333400-169336000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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