Variant report

Variant	rs72831633
Chromosome Location	chr2:112945932-112945933
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:112941329..112944537-chr2:112945158..112947736,3	K562	blood:
2	chr2:112945476..112947826-chr2:112951258..112953580,3	MCF-7	breast:
3	chr2:112940652..112943240-chr2:112945520..112948654,3	K562	blood:
4	chr2:112944701..112946678-chr2:112951279..112953593,2	K562	blood:
5	chr2:112944016..112946935-chr2:113032135..113034643,2	K562	blood:

Variant related genes	Relation type
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10864901	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11123130	1.00[ASN][1000 genomes]
rs11123133	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11676628	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679986	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11682795	0.91[AMR][1000 genomes]
rs11685462	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11685514	0.91[AMR][1000 genomes]
rs11687980	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11688511	0.84[AMR][1000 genomes]
rs11689858	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11691239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693294	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11695974	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11903915	1.00[ASN][1000 genomes]
rs12474447	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12477879	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12711736	0.89[ASN][1000 genomes]
rs4516428	0.84[AMR][1000 genomes]
rs4848281	0.89[ASN][1000 genomes]
rs4849051	0.89[ASN][1000 genomes]
rs55798617	0.86[EUR][1000 genomes]
rs55802705	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55821286	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55861985	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56044884	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56048537	0.84[AMR][1000 genomes]
rs6708607	1.00[ASN][1000 genomes]
rs6711180	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6722612	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6747639	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6759283	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6761440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72831641	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831642	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72831649	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831651	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831658	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831660	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831662	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831664	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72831685	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72831688	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72833410	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72833412	0.84[AMR][1000 genomes]
rs72833413	0.84[AMR][1000 genomes]
rs72833414	0.91[AMR][1000 genomes]
rs72833415	0.84[AMR][1000 genomes]
rs72833428	0.84[AMR][1000 genomes]
rs72833432	0.84[AMR][1000 genomes]
rs7586893	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7587316	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7596661	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7599551	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS 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	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv874866	chr2:112906599-112991098	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv874867	chr2:112930064-113038409	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs72831633	RGPD8	cis	Nerve Tibial	GTEx
rs72831633	RGPD8	cis	Artery Tibial	GTEx
rs72831633	RGPD8	cis	Whole Blood	GTEx
rs72831633	RGPD8	cis	Adipose Subcutaneous	GTEx
rs72831633	RGPD8	cis	lung	GTEx
rs72831633	RGPD8	cis	Muscle Skeletal	GTEx
rs72831633	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs72831633	RGPD8	cis	Heart Left Ventricle	GTEx
rs72831633	RGPD8	cis	Esophagus Mucosa	GTEx
rs72831633	RGPD8	cis	Artery Aorta	GTEx
rs72831633	RGPD8	cis	Esophagus Muscularis	GTEx
rs72831633	RGPD8	cis	Thyroid	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112914600-112972800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:112939600-112946400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:112939600-112946600	Weak transcription	Gastric	stomach
4	chr2:112940400-112946400	Weak transcription	Right Ventricle	heart
5	chr2:112941000-112946000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:112943200-112952200	Weak transcription	Fetal Lung	lung
7	chr2:112943400-112948200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr2:112944800-112946600	Enhancers	Primary B cells from peripheral blood	blood
9	chr2:112944800-112946600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:112944800-112946800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr2:112944800-112947000	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr2:112945000-112946200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr2:112945000-112946200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr2:112945000-112946200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr2:112945000-112946200	Enhancers	Dnd41	blood
16	chr2:112945200-112946000	Enhancers	GM12878-XiMat	blood
17	chr2:112945200-112946200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr2:112945200-112946400	Enhancers	Primary hematopoietic stem cells	blood
19	chr2:112945200-112946600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:112945200-112946800	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr2:112945200-112947000	Enhancers	Fetal Thymus	thymus
22	chr2:112945200-112970600	Weak transcription	Fetal Stomach	stomach
23	chr2:112945400-112946000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:112945400-112946000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr2:112945400-112946200	Enhancers	HMEC	breast
26	chr2:112945400-112946200	Enhancers	NHEK	skin
27	chr2:112945400-112946400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:112945400-112947000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:112945600-112946000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:112945600-112946000	Flanking Active TSS	HUVEC	blood vessel
31	chr2:112945600-112946000	Flanking Active TSS	K562	blood
32	chr2:112945600-112946000	Enhancers	NH-A	brain
33	chr2:112945600-112946200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:112945600-112946200	Flanking Active TSS	Thymus	Thymus
35	chr2:112945600-112946600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr2:112945600-112948600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:112945800-112946200	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:112945800-112946200	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr2:112945800-112951600	Weak transcription	Fetal Muscle Leg	muscle

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