Variant report

Variant	rs9287089
Chromosome Location	chr1:169451694-169451695
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	chr1:169451630-169451883	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169428536..169430863-chr1:169451257..169453654,2	K562	blood:
2	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
3	chr1:169429762..169432470-chr1:169449878..169451863,2	MCF-7	breast:
4	chr1:169437031..169439523-chr1:169451162..169453352,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213062	TF binding region
ENSG00000198734	Chromatin interaction
ENSG00000117477	Chromatin interaction
ENSG00000234437	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10919168	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10919174	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1208134	0.87[ASN][1000 genomes]
rs1208135	0.87[ASN][1000 genomes]
rs1517744	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1517747	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1983546	0.93[ASN][1000 genomes]
rs6656822	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6700375	0.89[AMR][1000 genomes];0.87[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	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
2	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
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005941	chr1:169410486-169456393	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9287089	NME7	cis	Thyroid	GTEx
rs9287089	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169430000-169452000	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr1:169430000-169452000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:169430000-169452600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:169430000-169452800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:169430000-169452800	Weak transcription	Brain Germinal Matrix	brain
6	chr1:169430000-169452800	Weak transcription	HMEC	breast
7	chr1:169430000-169452800	Weak transcription	NHDF-Ad	bronchial
8	chr1:169430000-169452800	Weak transcription	NHEK	skin
9	chr1:169430000-169453400	Weak transcription	Colonic Mucosa	Colon
10	chr1:169430000-169453800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:169430000-169454000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:169430000-169454400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:169430000-169454400	Weak transcription	Spleen	Spleen
14	chr1:169430200-169451800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:169430200-169452600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:169430200-169452600	Weak transcription	NH-A	brain
17	chr1:169430200-169453200	Weak transcription	Esophagus	oesophagus
18	chr1:169430600-169452800	Weak transcription	Small Intestine	intestine
19	chr1:169431200-169452000	Weak transcription	GM12878-XiMat	blood
20	chr1:169434600-169452600	Weak transcription	Primary B cells from cord blood	blood
21	chr1:169435200-169452800	Weak transcription	Fetal Kidney	kidney
22	chr1:169437400-169452600	Weak transcription	HSMMtube	muscle
23	chr1:169437400-169452600	Weak transcription	Osteobl	bone
24	chr1:169437400-169452800	Weak transcription	Aorta	Aorta
25	chr1:169437400-169452800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:169437800-169452600	Weak transcription	Fetal Brain Female	brain
27	chr1:169438600-169452200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:169438600-169453200	Weak transcription	Fetal Lung	lung
29	chr1:169438800-169452600	Weak transcription	HSMM	muscle
30	chr1:169439200-169452000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:169439600-169452600	Weak transcription	Primary T cells from cord blood	blood
32	chr1:169443000-169452800	Weak transcription	A549	lung
33	chr1:169443800-169452800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:169444200-169451800	Weak transcription	Brain Substantia Nigra	brain
35	chr1:169444200-169454000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:169444600-169452600	Weak transcription	Stomach Mucosa	stomach
37	chr1:169444600-169452800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:169446600-169453000	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:169446800-169452000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr1:169446800-169452000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:169446800-169452000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:169446800-169452000	Weak transcription	Dnd41	blood
43	chr1:169446800-169452400	Weak transcription	Brain Anterior Caudate	brain
44	chr1:169446800-169452600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:169446800-169452600	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:169446800-169452600	Weak transcription	Placenta	Placenta
47	chr1:169446800-169452600	Weak transcription	Fetal Stomach	stomach
48	chr1:169446800-169452800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:169446800-169452800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:169446800-169452800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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