Variant report

Variant	rs7556463
Chromosome Location	chr1:169295842-169295843
allele	A/T
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	E2F4	chr1:169295682-169295871	MCF10A-Er-Src	breast:	n/a	n/a
2	KAP1	chr1:169295661-169296277	K562	blood:	n/a	n/a
3	MYC	chr1:169295566-169296401	K562	blood:	n/a	n/a
4	GATA1	chr1:169295736-169296662	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169279086..169281627-chr1:169295579..169298053,2	K562	blood:
2	chr1:169291437..169294345-chr1:169295475..169297579,2	K562	blood:

Variant related genes	Relation type
NME7	TF binding region
ENSG00000143156	Chromatin interaction
ENSG00000235575	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1011638	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1018832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10458388	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10458394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10489190	1.00[AFR][1000 genomes]
rs10489417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10494477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10494478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs10737545	1.00[ASN][1000 genomes]
rs10800429	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10800431	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10800432	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10800433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800434	1.00[ASN][1000 genomes]
rs10919070	1.00[JPT][hapmap]
rs10919071	1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap]
rs10919085	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10919087	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10919093	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10919122	1.00[AFR][1000 genomes]
rs10919123	1.00[AFR][1000 genomes]
rs10919125	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919127	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919128	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919129	0.83[AMR][1000 genomes]
rs10919130	1.00[ASN][1000 genomes]
rs10919133	1.00[ASN][1000 genomes]
rs10919134	1.00[ASN][1000 genomes]
rs10919135	1.00[ASN][1000 genomes]
rs10919144	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10919147	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10919149	1.00[AFR][1000 genomes]
rs10919150	1.00[AFR][1000 genomes]
rs10919153	1.00[AFR][1000 genomes]
rs10919158	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs10919162	1.00[AFR][1000 genomes]
rs10919165	1.00[AFR][1000 genomes]
rs12021696	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12022617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs12022768	1.00[AFR][1000 genomes]
rs12025397	1.00[AFR][1000 genomes]
rs12025566	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12025721	1.00[AFR][1000 genomes]
rs12025910	1.00[ASW][hapmap]
rs12028197	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12028208	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs12029800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12030541	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12030810	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031371	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031830	1.00[ASN][1000 genomes]
rs12035622	1.00[JPT][hapmap]
rs12036426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12037926	1.00[AFR][1000 genomes]
rs12042082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12042990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12044982	1.00[AFR][1000 genomes]
rs12045803	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048188	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12401962	1.00[AFR][1000 genomes]
rs12401966	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12402774	1.00[AFR][1000 genomes]
rs12403181	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12405185	1.00[AFR][1000 genomes]
rs12405725	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes]
rs12408636	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12410241	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12410387	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12410456	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12410548	0.89[EUR][1000 genomes]
rs12567342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1517742	1.00[AFR][1000 genomes]
rs1517746	1.00[AFR][1000 genomes]
rs1517749	1.00[ASN][1000 genomes]
rs1517750	1.00[ASN][1000 genomes]
rs17345156	1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap]
rs17345426	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17345531	1.00[AFR][1000 genomes]
rs17349677	1.00[AFR][1000 genomes]
rs17518147	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes]
rs17576927	1.00[AFR][1000 genomes]
rs1856302	1.00[ASN][1000 genomes]
rs1894691	1.00[ASW][hapmap]
rs1894703	1.00[ASW][hapmap]
rs2000321	1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap]
rs2001155	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2001156	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2090514	1.00[ASN][1000 genomes]
rs2092083	1.00[AFR][1000 genomes]
rs34323371	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3766074	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3766101	1.00[AFR][1000 genomes]
rs4497270	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4534447	1.00[ASN][1000 genomes]
rs4562680	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6013	1.00[ASW][hapmap]
rs6027	1.00[ASW][hapmap]
rs61806987	1.00[ASN][1000 genomes]
rs72704035	1.00[AFR][1000 genomes]
rs72706084	1.00[AFR][1000 genomes]
rs7413522	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7414819	1.00[AFR][1000 genomes]
rs7522565	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7528142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929132	1.00[ASN][1000 genomes]
rs9332661	1.00[ASW][hapmap]
rs9887925	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv429913	chr1:169177019-169296744	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv1012919	chr1:169200982-169324750	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7556463	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169260400-169310400	Weak transcription	Fetal Stomach	stomach
2	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
3	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:169271800-169297200	Weak transcription	Psoas Muscle	Psoas
5	chr1:169273600-169312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:169276800-169304600	Weak transcription	Ovary	ovary
7	chr1:169277000-169306200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:169279200-169296000	Weak transcription	Primary T cells from cord blood	blood
9	chr1:169280200-169304600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:169281600-169306600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:169282000-169306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:169288600-169297200	Weak transcription	Small Intestine	intestine
13	chr1:169291000-169296200	Weak transcription	NHDF-Ad	bronchial
14	chr1:169291000-169313200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:169291200-169296000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:169291400-169296000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:169291400-169296000	Weak transcription	Osteobl	bone
18	chr1:169294000-169305200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:169294600-169297600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr1:169294600-169307400	Weak transcription	Gastric	stomach
21	chr1:169294800-169297200	Weak transcription	Left Ventricle	heart
22	chr1:169294800-169299600	Weak transcription	Fetal Intestine Small	intestine
23	chr1:169295400-169296200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:169295400-169296600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr1:169295400-169296600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:169295400-169297400	Enhancers	Primary hematopoietic stem cells	blood
27	chr1:169295600-169296000	Enhancers	Adipose Nuclei	Adipose
28	chr1:169295600-169296000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr1:169295600-169296200	Enhancers	Primary B cells from peripheral blood	blood
30	chr1:169295600-169296200	Enhancers	Hela-S3	cervix
31	chr1:169295600-169296600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:169295600-169296600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:169295600-169296600	Flanking Active TSS	A549	lung
34	chr1:169295600-169296600	Enhancers	HMEC	breast
35	chr1:169295600-169296600	Flanking Active TSS	HUVEC	blood vessel
36	chr1:169295600-169296600	Enhancers	NH-A	brain
37	chr1:169295800-169296000	Flanking Active TSS	K562	blood
38	chr1:169295800-169296600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:169295800-169296600	Enhancers	GM12878-XiMat	blood
40	chr1:169295800-169296800	Enhancers	NHEK	skin
41	chr1:169295800-169297200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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