Variant report

Variant	rs72831634
Chromosome Location	chr2:112946796-112946797
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

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	chr2:112939127..112941116-chr2:112946506..112948425,2	MCF-7	breast:
5	chr2:112944016..112946935-chr2:113032135..113034643,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FBLN7-2	chr2:112945941-112948212	NONHSAT073684

No data

Variant related genes	Relation type
ENSG00000188177	Chromatin interaction
ENSG00000144152	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]
rs72831633	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
rs72831634	RGPD8	cis	Artery Aorta	GTEx
rs72831634	RGPD8	cis	Thyroid	GTEx
rs72831634	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs72831634	RGPD8	cis	lung	GTEx
rs72831634	RGPD8	cis	Heart Left Ventricle	GTEx
rs72831634	RGPD8	cis	Artery Tibial	GTEx
rs72831634	RGPD8	cis	Muscle Skeletal	GTEx
rs72831634	RGPD8	cis	Adipose Subcutaneous	GTEx
rs72831634	RGPD8	cis	Esophagus Mucosa	GTEx
rs72831634	RGPD8	cis	Whole Blood	GTEx
rs72831634	RGPD8	cis	Esophagus Muscularis	GTEx
rs72831634	RGPD8	cis	Nerve Tibial	GTEx

Chromatin state (count:24 , 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	chr2:112943200-112952200	Weak transcription	Fetal Lung	lung
3	chr2:112943400-112948200	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr2:112944800-112946800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr2:112944800-112947000	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr2:112945200-112946800	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr2:112945200-112947000	Enhancers	Fetal Thymus	thymus
8	chr2:112945200-112970600	Weak transcription	Fetal Stomach	stomach
9	chr2:112945400-112947000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:112945600-112948600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:112945800-112951600	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:112946000-112946800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:112946000-112947000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:112946000-112947000	Enhancers	HUVEC	blood vessel
15	chr2:112946000-112947200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:112946200-112947000	Enhancers	Thymus	Thymus
17	chr2:112946200-112947200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr2:112946200-112948400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr2:112946200-112948600	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr2:112946400-112948200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:112946400-112951800	Weak transcription	K562	blood
22	chr2:112946400-112953800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr2:112946600-112947800	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr2:112946600-112950800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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