Variant report

Variant	rs684996
Chromosome Location	chr1:78666554-78666555
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs11162418	0.83[ASN][1000 genomes]
rs11162420	0.81[ASN][1000 genomes]
rs11162421	0.83[ASN][1000 genomes]
rs11162422	0.81[ASN][1000 genomes]
rs11162423	0.81[ASN][1000 genomes]
rs11162433	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11584032	0.83[ASN][1000 genomes]
rs12082228	0.82[ASN][1000 genomes]
rs12083265	0.83[ASN][1000 genomes]
rs12131414	0.83[ASN][1000 genomes]
rs12749252	0.83[ASN][1000 genomes]
rs1359043	0.83[ASN][1000 genomes]
rs1407747	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1407748	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1621088	0.83[ASN][1000 genomes]
rs1625234	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1770306	0.84[ASN][1000 genomes]
rs1770307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2025610	0.83[ASN][1000 genomes]
rs2025611	0.83[ASN][1000 genomes]
rs2209472	0.83[ASN][1000 genomes]
rs2351907	0.83[ASN][1000 genomes]
rs2351909	0.83[ASN][1000 genomes]
rs2351910	0.83[ASN][1000 genomes]
rs2882796	0.81[ASN][1000 genomes]
rs2882797	0.81[ASN][1000 genomes]
rs2882798	0.83[ASN][1000 genomes]
rs4258183	0.83[ASN][1000 genomes]
rs4258184	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4268312	0.83[ASN][1000 genomes]
rs4285658	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4396076	0.82[ASN][1000 genomes]
rs4529663	0.83[ASN][1000 genomes]
rs4587522	0.83[ASN][1000 genomes]
rs4650313	0.83[ASN][1000 genomes]
rs4650315	0.83[ASN][1000 genomes]
rs4650607	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs488469	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs494496	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs501774	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs513245	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs513977	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs521029	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs523751	0.84[ASN][1000 genomes]
rs526723	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs531841	0.82[ASN][1000 genomes]
rs554298	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs557688	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs558643	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs561289	0.91[ASN][1000 genomes]
rs577978	1.00[ASW][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs580426	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs581926	0.82[ASN][1000 genomes]
rs582281	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs582395	0.84[ASN][1000 genomes]
rs582795	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs584660	0.94[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs585100	0.93[ASW][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs58611517	0.83[ASN][1000 genomes]
rs591343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593652	0.83[ASN][1000 genomes]
rs597063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597272	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs599386	0.82[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs599730	0.81[ASW][hapmap]
rs600781	0.84[ASN][1000 genomes]
rs605659	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs609359	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs609390	0.86[JPT][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs610508	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs612486	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs614836	0.93[CEU][hapmap];0.80[AMR][1000 genomes]
rs614963	0.94[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs61777350	0.82[ASN][1000 genomes]
rs618063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs618551	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs618581	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs618593	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs624766	0.91[ASN][1000 genomes]
rs627493	0.84[ASN][1000 genomes]
rs627549	0.84[ASN][1000 genomes]
rs627661	0.94[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs629947	0.84[ASN][1000 genomes]
rs633227	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs633664	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs633769	0.82[AFR][1000 genomes]
rs634741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs637943	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs642248	0.93[ASW][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6424716	0.83[ASN][1000 genomes]
rs6424717	0.83[ASN][1000 genomes]
rs644332	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs644359	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs647809	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs648315	0.91[AMR][1000 genomes]
rs649502	0.84[ASN][1000 genomes]
rs656372	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs658212	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs659902	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs663254	0.93[ASW][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.80[MKK][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6665090	0.86[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs672391	0.91[ASN][1000 genomes]
rs674933	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs675799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs677875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680143	0.86[ASN][1000 genomes]
rs680971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681907	0.85[MEX][hapmap]
rs683097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs684657	0.80[ASN][1000 genomes]
rs687708	0.93[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs699009	0.91[ASN][1000 genomes]
rs7367729	0.80[ASN][1000 genomes]
rs7367884	0.84[ASN][1000 genomes]
rs7417073	0.83[ASN][1000 genomes]
rs7515450	0.84[ASN][1000 genomes]
rs7518152	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7532752	0.83[ASN][1000 genomes]
rs7555504	0.83[ASN][1000 genomes]
rs812097	0.81[CEU][hapmap]
rs9425188	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv546600	chr1:78649862-78666990	Active TSS Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs684996	NEXN	cis	lymphoblastoid	seeQTL
rs684996	DNAJB4	cis	parietal	SCAN
rs684996	LHX8	cis	parietal	SCAN
rs684996	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78656600-78668800	Weak transcription	Liver	Liver
2	chr1:78657600-78667200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:78657600-78669600	Weak transcription	Pancreas	Pancrea
4	chr1:78659400-78668000	Weak transcription	Fetal Intestine Small	intestine
5	chr1:78665400-78666600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:78666200-78667400	Enhancers	Stomach Smooth Muscle	stomach
7	chr1:78666400-78667400	Enhancers	Colon Smooth Muscle	Colon
8	chr1:78666400-78667800	Enhancers	Rectal Smooth Muscle	rectum
9	chr1:78666400-78668200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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