Variant report

Variant	rs1124843
Chromosome Location	chr1:169369458-169369459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169363269..169365266-chr1:169367448..169370534,3	K562	blood:
2	chr1:169353969..169356305-chr1:169367810..169369890,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1018831	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10429893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465575	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465576	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489189	0.96[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];0.84[EUR][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];0.85[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]
rs1133814	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024897	0.85[CEU][hapmap]
rs12029566	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076993	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208134	0.81[ASN][1000 genomes]
rs1208135	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1208370	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1208377	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.81[YRI][hapmap]
rs12563090	0.85[CEU][hapmap]
rs1400836	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
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	0.96[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.99[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];0.84[EUR][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	0.96[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];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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];0.99[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	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[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	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[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];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[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	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7539415	0.85[CEU][hapmap]
rs7544221	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554689	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs760603	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925892	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs932301	0.96[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	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
3	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1124843	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs1124843	C1orf114	cis	parietal	SCAN
rs1124843	NME7	cis	Artery Tibial	GTEx
rs1124843	NME7	cis	Esophagus Muscularis	GTEx
rs1124843	KIFAP3	cis	cerebellum	SCAN
rs1124843	SELP	cis	cerebellum	SCAN
rs1124843	C1orf114	cis	cerebellum	SCAN
rs1124843	NME7	cis	Thyroid	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169353000-169369800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:169354000-169370000	Weak transcription	Aorta	Aorta
3	chr1:169354800-169370600	Weak transcription	Fetal Kidney	kidney
4	chr1:169359600-169369800	Weak transcription	NHDF-Ad	bronchial
5	chr1:169360600-169372200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:169360800-169370600	Weak transcription	NHLF	lung
7	chr1:169360800-169395200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:169362200-169370000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:169362200-169370000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:169362200-169371200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:169362400-169369800	Weak transcription	Fetal Thymus	thymus
12	chr1:169362400-169370000	Weak transcription	Brain Germinal Matrix	brain
13	chr1:169362400-169370000	Weak transcription	Fetal Brain Female	brain
14	chr1:169362600-169369600	Weak transcription	Primary T cells from cord blood	blood
15	chr1:169363400-169371200	Weak transcription	Ovary	ovary
16	chr1:169364400-169375600	Weak transcription	Brain Anterior Caudate	brain
17	chr1:169365400-169370200	Weak transcription	NH-A	brain
18	chr1:169365600-169370800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:169365600-169371000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:169365600-169371200	Weak transcription	Fetal Lung	lung
21	chr1:169365800-169372400	Weak transcription	HSMM	muscle
22	chr1:169366000-169370400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:169366200-169369600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:169366200-169370000	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr1:169367400-169370000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:169367400-169370200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:169368200-169371000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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