Variant report

Variant	rs1400836
Chromosome Location	chr1:169397137-169397138
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	MXI1	chr1:169395460-169397375	SK-N-SH	brain:	n/a	chr1:169396806-169396821

Variant related genes	Relation type
CCDC181	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10429893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465575	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10465576	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732287	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs10737546	0.81[YRI][hapmap]
rs10753786	0.82[ASW][hapmap];0.89[YRI][hapmap]
rs10800424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs10800425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs10800435	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes]
rs10800438	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10800440	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800441	0.85[CEU][hapmap]
rs10800447	0.81[YRI][hapmap]
rs10919120	0.88[CHD][hapmap]
rs10919124	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10919132	0.82[ASW][hapmap];0.89[YRI][hapmap]
rs10919168	0.81[ASN][1000 genomes]
rs10919174	0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs1124843	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133814	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024897	0.85[CEU][hapmap]
rs12029566	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12076993	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208134	0.81[ASN][1000 genomes]
rs1208135	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12563090	0.85[CEU][hapmap]
rs1517744	0.87[CHD][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1517747	0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1591733	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.85[YRI][hapmap]
rs1856303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1914505	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980198	0.85[CEU][hapmap]
rs1983546	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs2003653	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037250	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2138898	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176473	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2275299	0.85[CEU][hapmap]
rs2300158	0.89[YRI][hapmap]
rs3766095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3818844	0.85[CEU][hapmap]
rs3820059	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3905328	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4264046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs4656183	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656670	0.85[CEU][hapmap]
rs4656672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427185	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[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs6427187	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656822	0.87[CHD][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.82[AMR][1000 genomes]
rs6669741	0.85[CEU][hapmap]
rs6669901	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672589	0.81[YRI][hapmap]
rs6677410	0.85[CEU][hapmap]
rs6696810	0.85[CEU][hapmap]
rs6700375	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7415756	0.89[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521582	1.00[CHD][hapmap]
rs7533257	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap]
rs7534737	0.85[CEU][hapmap]
rs7535765	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7539415	0.85[CEU][hapmap]
rs7544221	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554689	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs760603	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925892	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs932301	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs994986	1.00[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1400836	NME7	cis	Thyroid	GTEx
rs1400836	C1orf114	cis	parietal	SCAN
rs1400836	C1orf114	cis	cerebellum	SCAN
rs1400836	NME7	cis	Artery Tibial	GTEx
rs1400836	NME7	cis	Esophagus Muscularis	GTEx
rs1400836	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs1400836	SELP	cis	cerebellum	SCAN
rs1400836	KIFAP3	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169394800-169397200	Active TSS	Brain Germinal Matrix	brain
2	chr1:169394800-169397200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr1:169395200-169397200	Active TSS	Brain Angular Gyrus	brain
4	chr1:169395200-169397200	Active TSS	Brain Cingulate Gyrus	brain
5	chr1:169395200-169397200	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr1:169395200-169397200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:169395400-169397200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:169395400-169397200	Active TSS	Brain Hippocampus Middle	brain
9	chr1:169395400-169397200	Active TSS	Brain Substantia Nigra	brain
10	chr1:169395400-169397200	Active TSS	Fetal Brain Female	brain
11	chr1:169395400-169397200	Active TSS	Ovary	ovary
12	chr1:169395400-169397200	Active TSS	Right Atrium	heart
13	chr1:169395400-169397200	Active TSS	NHLF	lung
14	chr1:169395600-169397200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:169395600-169397200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:169395600-169397200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:169395600-169397200	Active TSS	Fetal Brain Male	brain
18	chr1:169395600-169397200	Active TSS	Fetal Kidney	kidney
19	chr1:169395800-169397200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:169396000-169397200	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr1:169396000-169397200	Active TSS	H1 Cell Line	embryonic stem cell
22	chr1:169396000-169397200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:169396000-169397200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:169396000-169397200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr1:169396000-169397200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:169396000-169397200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:169396000-169397200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:169396000-169397200	Active TSS	HSMMtube	muscle
29	chr1:169396000-169397400	Active TSS	Brain Anterior Caudate	brain
30	chr1:169396000-169397400	Flanking Active TSS	Dnd41	blood
31	chr1:169396200-169397200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:169396200-169397200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:169396200-169397200	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr1:169396200-169397200	Active TSS	Muscle Satellite Cultured Cells	--
35	chr1:169396200-169397200	Active TSS	HSMM	muscle
36	chr1:169396200-169397200	Bivalent/Poised TSS	NHDF-Ad	bronchial
37	chr1:169396200-169397400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
38	chr1:169396400-169397200	Active TSS	Primary T cells from cord blood	blood
39	chr1:169396400-169397200	Bivalent/Poised TSS	Fetal Stomach	stomach
40	chr1:169396600-169397200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:169396600-169397200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:169396600-169397200	Active TSS	Thymus	Thymus
43	chr1:169396800-169397200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:169396800-169397200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
45	chr1:169396800-169397200	Bivalent/Poised TSS	Primary B cells from cord blood	blood
46	chr1:169396800-169397200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:169396800-169397200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:169396800-169397200	Active TSS	Colon Smooth Muscle	Colon
49	chr1:169396800-169397200	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr1:169396800-169397200	Active TSS	Fetal Muscle Leg	muscle

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