Variant report

Variant	rs7524348
Chromosome Location	chr1:169430438-169430439
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10429893	0.81[ASN][1000 genomes]
rs10465575	0.81[ASN][1000 genomes]
rs10465576	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10489189	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10737546	0.83[EUR][1000 genomes]
rs10800438	0.81[ASN][1000 genomes]
rs10800440	0.81[ASN][1000 genomes]
rs10800447	1.00[CEU][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs10919168	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919173	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10919174	0.92[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1124843	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1133814	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12029566	0.81[ASN][1000 genomes]
rs12076993	0.82[AMR][1000 genomes]
rs1208134	1.00[ASN][1000 genomes]
rs1208135	1.00[ASN][1000 genomes]
rs1400836	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1517743	0.82[EUR][1000 genomes]
rs1517744	0.92[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517745	0.96[CEU][hapmap]
rs1517747	0.92[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1914505	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1983546	0.93[ASN][1000 genomes]
rs2003653	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2138898	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2176473	0.81[ASN][1000 genomes]
rs3820059	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3905328	0.81[ASN][1000 genomes]
rs4656183	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4656672	0.81[ASN][1000 genomes]
rs6427187	0.81[ASN][1000 genomes]
rs6656822	0.96[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6669901	0.81[ASN][1000 genomes]
rs6672589	1.00[CEU][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs6697727	0.82[EUR][1000 genomes]
rs6700375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415756	0.81[ASN][1000 genomes]
rs7544221	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs760603	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs925892	0.81[ASN][1000 genomes]
rs9287089	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs932301	0.82[AMR][1000 genomes];0.81[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
rs7524348	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs7524348	NME7	cis	Thyroid	GTEx

Chromatin state (count:90 , 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	chr1:169430000-169430600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:169430000-169431200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr1:169430000-169434000	Weak transcription	HSMM	muscle
11	chr1:169430000-169434400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:169430000-169434600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:169430000-169434600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:169430000-169434600	Weak transcription	Left Ventricle	heart
15	chr1:169430000-169434600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:169430000-169434600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:169430000-169435000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:169430000-169435200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:169430000-169435200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:169430000-169436000	Weak transcription	Brain Anterior Caudate	brain
21	chr1:169430000-169436200	Weak transcription	Primary T cells from cord blood	blood
22	chr1:169430000-169436200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:169430000-169436400	Weak transcription	Fetal Thymus	thymus
24	chr1:169430000-169443800	Weak transcription	Brain Substantia Nigra	brain
25	chr1:169430000-169444800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:169430000-169445600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:169430000-169445600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:169430000-169446200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:169430000-169446200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr1:169430000-169446200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:169430000-169446400	Weak transcription	HUVEC	blood vessel
32	chr1:169430000-169450000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:169430000-169452000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:169430000-169452000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:169430000-169452600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:169430000-169452800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:169430000-169452800	Weak transcription	Brain Germinal Matrix	brain
38	chr1:169430000-169452800	Weak transcription	HMEC	breast
39	chr1:169430000-169452800	Weak transcription	NHDF-Ad	bronchial
40	chr1:169430000-169452800	Weak transcription	NHEK	skin
41	chr1:169430000-169453400	Weak transcription	Colonic Mucosa	Colon
42	chr1:169430000-169453800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:169430000-169454000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:169430000-169454400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:169430000-169454400	Weak transcription	Spleen	Spleen
46	chr1:169430200-169430600	Enhancers	HepG2	liver
47	chr1:169430200-169430800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:169430200-169430800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:169430200-169431200	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr1:169430200-169431200	Enhancers	Liver	Liver

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