Variant report

Variant	rs2092083
Chromosome Location	chr1:169432479-169432480
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	chr1:169432466-169432869	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169431261..169433752-chr1:169476428..169478805,3	K562	blood:
2	chr1:169432008..169435585-chr1:169454180..169456077,3	MCF-7	breast:
3	chr1:169427119..169430164-chr1:169432459..169436469,3	K562	blood:

Variant related genes	Relation type
CCDC181	TF binding region
ENSG00000234437	TF binding region
ENSG00000213062	Chromatin interaction
ENSG00000234437	Chromatin interaction
ENSG00000117477	Chromatin interaction
ENSG00000117479	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10489190	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10489417	1.00[AFR][1000 genomes]
rs10494477	1.00[AFR][1000 genomes]
rs10494478	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[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]
rs10919149	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10919150	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10919153	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10919158	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10919162	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10919165	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10919172	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022617	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12022768	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12025397	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12025721	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12028208	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[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];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12042990	1.00[AFR][1000 genomes]
rs12044982	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12045803	1.00[AFR][1000 genomes]
rs12048188	1.00[AFR][1000 genomes]
rs12401962	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12402774	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405185	1.00[AFR][1000 genomes]
rs12405725	1.00[AFR][1000 genomes]
rs12567342	1.00[AFR][1000 genomes]
rs1517742	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517746	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17345426	1.00[AFR][1000 genomes]
rs17345531	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17349677	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17518147	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17576927	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1949426	0.93[ASN][1000 genomes]
rs2001156	1.00[AFR][1000 genomes]
rs3766100	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766101	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4497270	1.00[AFR][1000 genomes]
rs4562680	1.00[AFR][1000 genomes]
rs72704035	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72706084	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7414819	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7522565	1.00[ASN][1000 genomes]
rs7546361	1.00[ASN][1000 genomes]
rs7554853	0.93[ASN][1000 genomes]
rs7556463	1.00[AFR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2092083	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169429600-169434600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr1:169429600-169448200	Weak transcription	Fetal Heart	heart
3	chr1:169429800-169434400	Weak transcription	Placenta	Placenta
4	chr1:169429800-169436200	Weak transcription	Psoas Muscle	Psoas
5	chr1:169429800-169436200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:169429800-169436800	Weak transcription	Right Ventricle	heart
7	chr1:169429800-169446400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:169430000-169434000	Weak transcription	HSMM	muscle
9	chr1:169430000-169434400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:169430000-169434600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:169430000-169434600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:169430000-169434600	Weak transcription	Left Ventricle	heart
13	chr1:169430000-169434600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:169430000-169434600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:169430000-169435000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:169430000-169435200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:169430000-169435200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:169430000-169436000	Weak transcription	Brain Anterior Caudate	brain
19	chr1:169430000-169436200	Weak transcription	Primary T cells from cord blood	blood
20	chr1:169430000-169436200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:169430000-169436400	Weak transcription	Fetal Thymus	thymus
22	chr1:169430000-169443800	Weak transcription	Brain Substantia Nigra	brain
23	chr1:169430000-169444800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:169430000-169445600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:169430000-169445600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:169430000-169446200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:169430000-169446200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:169430000-169446200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:169430000-169446400	Weak transcription	HUVEC	blood vessel
30	chr1:169430000-169450000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:169430000-169452000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:169430000-169452000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:169430000-169452600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:169430000-169452800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:169430000-169452800	Weak transcription	Brain Germinal Matrix	brain
36	chr1:169430000-169452800	Weak transcription	HMEC	breast
37	chr1:169430000-169452800	Weak transcription	NHDF-Ad	bronchial
38	chr1:169430000-169452800	Weak transcription	NHEK	skin
39	chr1:169430000-169453400	Weak transcription	Colonic Mucosa	Colon
40	chr1:169430000-169453800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:169430000-169454000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:169430000-169454400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:169430000-169454400	Weak transcription	Spleen	Spleen
44	chr1:169430200-169434200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:169430200-169434400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:169430200-169434600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr1:169430200-169434600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:169430200-169434600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:169430200-169434600	Weak transcription	Adipose Nuclei	Adipose
50	chr1:169430200-169434600	Weak transcription	Duodenum Mucosa	Duodenum

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