Variant report

Variant	rs4899222
Chromosome Location	chr14:68199660-68199661
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	chr14:68198132..68200184-chr14:68201733..68204809,3	K562	blood:

Variant related genes	Relation type
ENSG00000271697	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10459532	0.83[CEU][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10483804	0.80[CEU][hapmap];0.84[TSI][hapmap]
rs1059238	0.83[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11158690	0.80[EUR][1000 genomes]
rs1120877	0.83[CEU][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11620761	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11622441	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11623700	1.00[ASW][hapmap];0.83[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11623711	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11623785	0.83[CEU][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11623961	0.83[CEU][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11624498	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11627201	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11628860	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12050393	1.00[ASW][hapmap];0.83[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1555193	0.83[CEU][hapmap];0.95[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17104490	0.82[ASW][hapmap];0.91[GIH][hapmap];0.86[LWK][hapmap]
rs17104526	0.85[AFR][1000 genomes]
rs17104544	0.82[ASW][hapmap];0.83[CEU][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17104550	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs17104597	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17104621	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249472	0.83[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17852293	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1955469	0.81[MEX][hapmap]
rs1955472	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1955473	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2234511	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2320029	0.95[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28873201	0.87[EUR][1000 genomes]
rs3742880	1.00[ASW][hapmap];0.83[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3742881	1.00[ASW][hapmap];0.95[GIH][hapmap];0.93[LWK][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3742882	0.81[MEX][hapmap];0.89[YRI][hapmap]
rs3742883	0.81[MEX][hapmap]
rs4899221	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902506	0.83[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4902508	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4902511	0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4902512	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55900323	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56244142	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60581344	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6573790	0.95[GIH][hapmap];1.00[MEX][hapmap]
rs6573794	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6573795	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7140310	0.83[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap]
rs7142897	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7144076	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7144124	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7151205	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7152326	0.89[YRI][hapmap]
rs7159889	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72723111	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72723115	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72723122	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72723126	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72723137	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72723144	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72723150	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72723152	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72723154	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72723155	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72723156	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72723158	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72723160	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72723163	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72723166	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72723167	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs742865	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742867	0.82[LWK][hapmap]
rs761513	1.00[ASW][hapmap];0.83[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs761514	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8009250	0.83[AFR][1000 genomes]
rs8013767	1.00[ASW][hapmap];0.83[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8017147	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8017326	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8019831	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8020591	0.81[CEU][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs932475	0.81[MEX][hapmap]

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	nsv902068	chr14:68083133-68204876	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1042536	chr14:68136913-68343198	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv542122	chr14:68136913-68343198	Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv521832	chr14:68141009-68204876	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4899222	RDH11	cis	Nerve Tibial	GTEx
rs4899222	RDH11	Cis_1M	lymphoblastoid	RTeQTL
rs4899222	ZBTB1	cis	cerebellum	SCAN
rs4899222	ATP6V1D	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68189000-68218800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr14:68189400-68200800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr14:68189800-68213400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr14:68194000-68202200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr14:68196200-68200600	Weak transcription	Brain Substantia Nigra	brain
6	chr14:68196200-68200600	Weak transcription	Lung	lung
7	chr14:68196200-68200600	Weak transcription	Pancreas	Pancrea
8	chr14:68196200-68219000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr14:68196800-68201400	Weak transcription	K562	blood
10	chr14:68196800-68214600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr14:68197200-68200400	Weak transcription	HepG2	liver
12	chr14:68197200-68201000	Weak transcription	Liver	Liver
13	chr14:68197200-68202000	Weak transcription	Stomach Mucosa	stomach
14	chr14:68197200-68214800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr14:68198400-68201400	Weak transcription	Brain Angular Gyrus	brain
16	chr14:68199400-68203800	Enhancers	Fetal Muscle Leg	muscle

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