Variant report

Variant	rs12590986
Chromosome Location	chr14:65357692-65357693
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:65353028..65355615-chr14:65356230..65358479,2	K562	blood:
2	chr14:65346776..65351606-chr14:65355142..65358604,5	K562	blood:
3	chr14:65356440..65358700-chr14:65379769..65381546,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125954	Chromatin interaction
ENSG00000258289	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 31 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10132858	0.83[CEU][hapmap]
rs10133054	0.84[CEU][hapmap]
rs10133290	0.84[CEU][hapmap]
rs10138534	0.84[CEU][hapmap]
rs10139595	0.84[CEU][hapmap]
rs10141986	0.84[CEU][hapmap];0.92[TSI][hapmap]
rs10143017	0.84[CEU][hapmap]
rs10148687	0.84[CEU][hapmap]
rs10151701	0.84[CEU][hapmap];0.92[TSI][hapmap]
rs10498518	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1064108	1.00[ASW][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs11158568	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11158569	0.84[CEU][hapmap];0.92[TSI][hapmap]
rs11622394	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11626982	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11627589	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11627688	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11848113	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12433639	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12433641	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12436747	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878229	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12878467	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12879744	0.82[AFR][1000 genomes]
rs12881353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12884463	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12889417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12890654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12891652	0.82[AFR][1000 genomes]
rs12897440	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475101	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs17102298	0.84[CEU][hapmap]
rs1951487	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951488	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951993	0.82[AFR][1000 genomes]
rs1957417	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1957418	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1957419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1957420	0.93[AFR][1000 genomes]
rs1957421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1957423	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1957425	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1957426	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147612	0.82[AFR][1000 genomes]
rs2147616	1.00[YRI][hapmap]
rs2296327	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs230702	0.81[CHB][hapmap]
rs2357867	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2357868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412065	0.84[CEU][hapmap];0.92[TSI][hapmap]
rs2737844	0.92[ASW][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs2898874	0.82[AFR][1000 genomes]
rs34201584	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34969442	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs35176965	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs422574	0.81[CHB][hapmap]
rs4243629	0.82[AFR][1000 genomes]
rs4899152	0.84[CEU][hapmap]
rs4899153	0.84[CEU][hapmap];0.92[TSI][hapmap]
rs4902332	0.84[CEU][hapmap]
rs4902333	0.87[CEU][hapmap]
rs4902334	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4902335	0.84[CEU][hapmap]
rs4902336	0.84[CEU][hapmap];0.92[TSI][hapmap]
rs4902339	0.82[AFR][1000 genomes]
rs4902343	0.84[CEU][hapmap]
rs4902345	0.84[CEU][hapmap]
rs4902346	0.84[CEU][hapmap]
rs6573585	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745	0.84[CEU][hapmap]
rs7143432	0.84[CEU][hapmap];0.92[TSI][hapmap]
rs7144811	0.84[CEU][hapmap];0.92[TSI][hapmap]
rs7151401	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7151780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7153990	0.85[CEU][hapmap]
rs7154406	0.84[CEU][hapmap]
rs743263	1.00[ASW][hapmap];0.88[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs743264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762071	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8016174	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs8019259	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8019750	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8019971	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8021590	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8021876	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8021998	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8022122	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693408	chr14:65292670-65358576	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv516238	chr14:65327288-65358576	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	esv3693169	chr14:65344400-65381068	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1311	chr14:65352722-65379802	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv510638	chr14:65353025-65368298	Enhancers Bivalent Enhancer Active TSS Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv993830	chr14:65357515-65363884	Enhancers Weak transcription Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:31)

SNP	Gene	Cis/trans	Tissue	Source
rs12590986	CHURC1	cis	Esophagus Mucosa	GTEx
rs12590986	CHURC1	cis	Cerebellum	GTEx
rs12590986	CHURC1	cis	Temporal Cortex	GTEx
rs12590986	CHURC1	cis	Whole Blood	GTEx
rs12590986	CHURC1	cis	lung	GTEx
rs12590986	C14orf52	cis	multi-tissue	Pritchard
rs12590986	CHURC1	cis	cerebellum	SCAN
rs12590986	RAB15	cis	cerebellum	SCAN
rs12590986	CHURC1	cis	lymphoblastoid	seeQTL
rs12590986	CHURC1	cis	Artery Tibial	GTEx
rs12590986	CHURC1	cis	Skin Sun Exposed Lower leg	GTEx
rs12590986	CHURC1	cis	Nerve Tibial	GTEx
rs12590986	CHURC1	cis	lesional skin	skin_eQTL
rs12590986	CHURC1	cis	Adipose Subcutaneous	GTEx
rs12590986	CHURC1	cis	normal skin	skin_eQTL
rs12590986	CHURC1	cis	Brain Pons	GTEx
rs12590986	RAB15	cis	lymphoblastoid	seeQTL
rs12590986	CHURC1	trans	brain	seeQTL
rs12590986	CHURC1	cis	Heart Left Ventricle	GTEx
rs12590986	CHURC1	cis	Muscle Skeletal	GTEx
rs12590986	CHURC1	cis	Lymphoblastoid	GTEx
rs12590986	CHURC1	cis	brain	seeQTL
rs12590986	CHURC1	Cis_1M	lymphoblastoid	RTeQTL
rs12590986	CHURC1	cis	Esophagus Muscularis	GTEx
rs12590986	CHURC1	cis	Thyroid	GTEx
rs12590986	CHURC1	cis	parietal	SCAN
rs12590986	CHURC1	cis	multi-tissue	Pritchard
rs12590986	CHURC1	cis	Frontal Cortex	GTEx
rs12590986	CHURC1	cis	uninvolved skin	skin_eQTL
rs12590986	IDO2	trans	parietal	SCAN
rs12590986	CHURC1	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65357400-65358600	Enhancers	K562	blood

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