Variant report

Variant	rs11687980
Chromosome Location	chr2:112991098-112991099
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr2:112990781-112991112	MCF10A-Er-Src	breast:	n/a	n/a
2	JUN	chr2:112990900-112991098	HepG2	liver:	n/a	chr2:112991031-112991040

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:112990251..112993065-chr2:113025836..113028410,2	K562	blood:
2	chr2:112989516..112991111-chr2:113030313..113033256,2	MCF-7	breast:

Variant related genes	Relation type
ZC3H8	TF binding region
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10864901	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11123133	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11676628	0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs11679986	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11682795	0.87[CEU][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11685462	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11685514	0.87[CEU][hapmap];0.93[GIH][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11688511	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11689858	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11691239	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11693294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11695974	0.87[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12474447	0.87[CEU][hapmap];0.93[GIH][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12477879	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4516428	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55798617	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55802705	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55821286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55861985	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56044884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56048537	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6711180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6722612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6747639	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6759283	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6761440	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831633	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831634	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831636	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831638	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831639	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72831641	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72831642	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72831649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72831651	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72831658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72831660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72831662	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72831664	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831685	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72833410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72833412	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72833413	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72833414	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72833415	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72833428	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72833431	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72833432	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7586893	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7587316	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7596661	0.87[CEU][hapmap];0.93[GIH][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7599551	0.93[CEU][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	esv1805614	chr2:112949713-113048705	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11687980	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs11687980	RGPD8	cis	Whole Blood	GTEx
rs11687980	RGPD8	cis	Artery Aorta	GTEx
rs11687980	RGPD8	cis	lung	GTEx
rs11687980	RGPD8	cis	Muscle Skeletal	GTEx
rs11687980	RGPD8	cis	Adipose Subcutaneous	GTEx
rs11687980	RGPD8	cis	Esophagus Mucosa	GTEx
rs11687980	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs11687980	RGPD8	cis	Esophagus Muscularis	GTEx
rs11687980	RGPD8	cis	Nerve Tibial	GTEx
rs11687980	RGPD8	cis	Artery Tibial	GTEx
rs11687980	RGPD8	cis	Thyroid	GTEx
rs11687980	RGPD8	cis	Heart Left Ventricle	GTEx
rs11687980	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112961000-113009000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:112968000-113011800	Weak transcription	Right Ventricle	heart
3	chr2:112968200-112999000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr2:112968200-113004000	Weak transcription	Fetal Brain Male	brain
5	chr2:112968200-113009200	Weak transcription	Small Intestine	intestine
6	chr2:112968200-113012000	Weak transcription	Pancreas	Pancrea
7	chr2:112968400-113003800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:112968800-113011400	Weak transcription	Brain Angular Gyrus	brain
9	chr2:112968800-113011800	Weak transcription	Brain Substantia Nigra	brain
10	chr2:112969000-112993000	Weak transcription	Colonic Mucosa	Colon
11	chr2:112969000-113005200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:112969200-112992000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:112969400-113011800	Weak transcription	Esophagus	oesophagus
14	chr2:112969600-113009000	Weak transcription	Psoas Muscle	Psoas
15	chr2:112970200-112992600	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:112970200-113004800	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:112970800-113003800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:112970800-113005200	Weak transcription	Gastric	stomach
19	chr2:112970800-113011600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:112971400-113011600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:112971800-113011800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:112973800-112993000	Weak transcription	HepG2	liver
23	chr2:112974000-112993800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:112974000-112993800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:112974000-112993800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:112974000-112994000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:112974000-113003600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:112974000-113004000	Weak transcription	Brain Anterior Caudate	brain
29	chr2:112974200-112993000	Weak transcription	Left Ventricle	heart
30	chr2:112978200-113006400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:112979000-113004400	Weak transcription	Lung	lung
32	chr2:112979600-113003200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:112979600-113004000	Weak transcription	Fetal Heart	heart
34	chr2:112979600-113011600	Weak transcription	Fetal Kidney	kidney
35	chr2:112979600-113012000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:112979800-112992600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:112980000-112991600	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr2:112980000-112993000	Weak transcription	Fetal Intestine Large	intestine
39	chr2:112980000-112993000	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:112980000-112993600	Weak transcription	Fetal Stomach	stomach
41	chr2:112980000-112993800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:112980000-112993800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:112980000-112993800	Weak transcription	Thymus	Thymus
44	chr2:112980000-112993800	Weak transcription	Spleen	Spleen
45	chr2:112980000-112994000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr2:112980000-113002400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:112980000-113003000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:112980000-113003600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:112980000-113004600	Weak transcription	Placenta	Placenta
50	chr2:112980000-113005400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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