Variant report

Variant	rs443009
Chromosome Location	chr20:25499817-25499818
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	chr20:25476823..25479458-chr20:25499157..25501846,2	MCF-7	breast:
2	chr20:25498962..25501422-chr20:25501455..25503650,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101004	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1047171	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs11087521	0.81[CEU][hapmap]
rs12428	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs13040726	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1541061	0.87[CEU][hapmap]
rs1983974	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2387881	0.91[GIH][hapmap]
rs2387976	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2856	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs34485039	0.89[ASN][1000 genomes]
rs35735333	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs372678	0.82[CEU][hapmap]
rs374701	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752273	1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs3761117	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs376742	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390123	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397119	0.93[GIH][hapmap]
rs398036	0.93[GIH][hapmap]
rs400357	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404148	0.89[CEU][hapmap]
rs404775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs417110	0.82[CEU][hapmap];0.93[GIH][hapmap]
rs417130	0.84[CEU][hapmap]
rs422148	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs424487	0.82[CEU][hapmap]
rs4280527	0.82[CEU][hapmap]
rs431579	0.82[CEU][hapmap];0.93[GIH][hapmap]
rs433352	0.82[CEU][hapmap];0.93[GIH][hapmap]
rs437635	0.81[CEU][hapmap]
rs4423675	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs442834	0.82[CEU][hapmap]
rs446649	0.82[CEU][hapmap];0.93[GIH][hapmap]
rs449370	0.82[CEU][hapmap];0.93[GIH][hapmap]
rs449801	0.93[CEU][hapmap]
rs4813562	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs4815411	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs4815412	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs4815413	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4815417	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs4815429	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815431	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815437	0.89[ASN][1000 genomes]
rs6037095	0.91[GIH][hapmap]
rs6037097	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs6037103	0.91[GIH][hapmap]
rs6037105	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs6037158	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050559	0.91[GIH][hapmap]
rs6050561	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs6050565	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs6050567	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs6050573	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs6050598	0.82[CEU][hapmap];0.93[GIH][hapmap]
rs6050599	0.81[CEU][hapmap]
rs6050617	0.82[CEU][hapmap]
rs6050626	0.80[CEU][hapmap];0.91[GIH][hapmap]
rs6050679	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076336	0.91[GIH][hapmap]
rs6076343	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076347	0.89[CEU][hapmap]
rs6076358	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076364	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6076366	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6076369	0.89[ASN][1000 genomes]
rs6083805	0.91[GIH][hapmap]
rs6083809	0.82[CEU][hapmap]
rs6083818	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs6083824	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6083828	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs6083845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083851	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083860	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083862	0.82[CEU][hapmap];0.86[GIH][hapmap]
rs6083891	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6107031	0.81[CEU][hapmap]
rs6107060	1.00[ASW][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6115156	0.85[AMR][1000 genomes]
rs6115159	0.81[CEU][hapmap]
rs6115188	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115200	0.82[CEU][hapmap]
rs6115210	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115214	0.82[CEU][hapmap]
rs6115215	0.82[CEU][hapmap]
rs6132845	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6132848	0.82[CEU][hapmap]
rs6138588	0.82[CEU][hapmap]
rs6138593	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138600	0.82[CEU][hapmap]
rs761025	0.81[CEU][hapmap]
rs84816	0.93[GIH][hapmap]
rs869358	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs928121	0.82[CEU][hapmap]
rs958075	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS 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	23 gene(s)	inside rSNPs	diseases
5	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv1062765	chr20:25466482-25556751	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv544225	chr20:25466482-25556751	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs443009	NINL	cis	Thyroid	GTEx
rs443009	ABHD12	cis	Temporal Cortex	GTEx
rs443009	ABHD12	cis	lesional skin	skin_eQTL
rs443009	HDHD4	cis	multi-tissue	Pritchard
rs443009	PYGB	cis	lymphoblastoid	seeQTL
rs443009	PYGB	cis	multi-tissue	Pritchard
rs443009	ABHD12	cis	Frontal Cortex	GTEx
rs443009	DCLRE1C	trans	multi-tissue	Pritchard
rs443009	ABHD12	cis	uninvolved skin	skin_eQTL
rs443009	ABHD12	trans	brain	seeQTL
rs443009	ABHD12	cis	Brain Pons	GTEx
rs443009	ABHD12	cis	brain	seeQTL
rs443009	ABHD12	cis	Cerebellum	GTEx
rs443009	ABHD12	cis	multi-tissue	Pritchard
rs443009	C20orf22	cis	multi-tissue	Pritchard
rs443009	ABHD12	cis	lymphoblastoid	seeQTL
rs443009	PYGB	cis	Whole Blood	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25489400-25505800	Weak transcription	NHDF-Ad	bronchial
2	chr20:25491200-25506200	Weak transcription	NHLF	lung
3	chr20:25493200-25512800	Weak transcription	Colon Smooth Muscle	Colon
4	chr20:25493600-25513000	Weak transcription	Left Ventricle	heart
5	chr20:25494000-25502000	ZNF genes & repeats	Dnd41	blood
6	chr20:25495600-25504800	Weak transcription	Osteobl	bone
7	chr20:25495800-25502200	Weak transcription	Stomach Mucosa	stomach
8	chr20:25495800-25506400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr20:25495800-25519400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr20:25496000-25512400	Weak transcription	Brain Angular Gyrus	brain
11	chr20:25496000-25513200	Weak transcription	HUVEC	blood vessel
12	chr20:25496400-25505800	Weak transcription	NH-A	brain
13	chr20:25496400-25506400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr20:25497400-25512400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr20:25497400-25512400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr20:25497400-25514800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr20:25497600-25502000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr20:25497600-25506400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr20:25497600-25507200	Weak transcription	Colonic Mucosa	Colon
20	chr20:25497600-25512600	Weak transcription	Fetal Heart	heart
21	chr20:25497800-25500200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr20:25497800-25506400	Weak transcription	HSMMtube	muscle
23	chr20:25497800-25512200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr20:25498000-25504800	Weak transcription	Lung	lung
25	chr20:25498000-25505800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr20:25498000-25506400	Weak transcription	Fetal Brain Male	brain
27	chr20:25498000-25506600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr20:25498000-25511000	Weak transcription	Brain Hippocampus Middle	brain
29	chr20:25498200-25501400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr20:25498200-25502000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr20:25498200-25502400	Weak transcription	Fetal Muscle Leg	muscle
32	chr20:25498200-25503200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr20:25498200-25503200	Weak transcription	Fetal Kidney	kidney
34	chr20:25498200-25503400	Weak transcription	Thymus	Thymus
35	chr20:25498200-25504000	Weak transcription	Fetal Intestine Small	intestine
36	chr20:25498200-25504000	Weak transcription	Fetal Stomach	stomach
37	chr20:25498200-25504800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr20:25498200-25504800	Weak transcription	Esophagus	oesophagus
39	chr20:25498200-25504800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr20:25498200-25505800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr20:25498200-25505800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr20:25498200-25505800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr20:25498200-25505800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr20:25498200-25505800	Weak transcription	Aorta	Aorta
45	chr20:25498200-25505800	Weak transcription	Spleen	Spleen
46	chr20:25498200-25506600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr20:25498200-25506600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr20:25498200-25507000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr20:25498200-25507000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr20:25498200-25510800	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links