Variant report

Variant	rs4516428
Chromosome Location	chr2:113072895-113072896
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113067314..113070627-chr2:113070650..113073571,3	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10864901	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11123133	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11679986	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11682795	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11685462	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11685514	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11687980	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11688511	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11689858	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11691239	0.84[AMR][1000 genomes]
rs11693294	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11695974	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12474447	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12477879	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13025468	0.85[CEU][hapmap]
rs55798617	0.87[EUR][1000 genomes]
rs55802705	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55821286	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55861985	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56044884	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56048537	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58360798	0.82[EUR][1000 genomes]
rs6542056	1.00[CEU][hapmap]
rs6711180	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6722612	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6729910	0.85[CEU][hapmap]
rs6747639	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6757757	0.86[CEU][hapmap]
rs6759275	0.85[CEU][hapmap]
rs6759283	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6761440	0.84[AMR][1000 genomes]
rs72831633	0.84[AMR][1000 genomes]
rs72831634	0.84[AMR][1000 genomes]
rs72831636	0.84[AMR][1000 genomes]
rs72831638	0.84[AMR][1000 genomes]
rs72831639	0.84[AMR][1000 genomes]
rs72831642	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72831649	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72831651	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72831658	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72831660	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72831662	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72831664	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831685	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72831688	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833410	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72833412	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72833413	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72833414	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72833415	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72833428	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72833431	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72833432	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7587316	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7596661	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7599551	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
4	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
5	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
6	nsv874868	chr2:113021811-113076095	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv874869	chr2:113021811-113089267	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv874870	chr2:113021811-113097699	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv874871	chr2:113021811-113217630	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv874873	chr2:113027569-113083367	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv874874	chr2:113027569-113089267	Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv874876	chr2:113051291-113089267	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4516428	RGPD8	cis	Esophagus Muscularis	GTEx
rs4516428	RGPD8	cis	Artery Aorta	GTEx
rs4516428	RGPD8	cis	Nerve Tibial	GTEx
rs4516428	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs4516428	RGPD8	cis	Whole Blood	GTEx
rs4516428	RGPD8	cis	Muscle Skeletal	GTEx
rs4516428	RGPD8	cis	Artery Tibial	GTEx
rs4516428	RGPD8	cis	lung	GTEx
rs4516428	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs4516428	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs4516428	ZC3H8	cis	Artery Tibial	GTEx
rs4516428	RGPD8	cis	Thyroid	GTEx
rs4516428	RGPD8	cis	Adipose Subcutaneous	GTEx
rs4516428	RGPD8	cis	Esophagus Mucosa	GTEx
rs4516428	RGPD8	cis	Heart Left Ventricle	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113034400-113097000	Weak transcription	Psoas Muscle	Psoas
2	chr2:113040000-113081800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:113046600-113079800	Weak transcription	Fetal Stomach	stomach
4	chr2:113048000-113084400	Weak transcription	Fetal Kidney	kidney
5	chr2:113048600-113081600	Weak transcription	Brain Anterior Caudate	brain
6	chr2:113048600-113081800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr2:113050600-113090600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:113051000-113088600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:113051600-113080600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:113051600-113081800	Weak transcription	Spleen	Spleen
11	chr2:113051600-113088600	Weak transcription	Esophagus	oesophagus
12	chr2:113051800-113081800	Weak transcription	Gastric	stomach
13	chr2:113051800-113081800	Weak transcription	Lung	lung
14	chr2:113053400-113074200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:113053400-113085400	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:113055400-113081800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:113056400-113089000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:113056800-113081800	Weak transcription	Fetal Brain Male	brain
19	chr2:113057000-113081800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr2:113057000-113099400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr2:113057400-113080600	Weak transcription	Fetal Brain Female	brain
22	chr2:113058000-113081800	Weak transcription	Pancreas	Pancrea
23	chr2:113058200-113074200	Weak transcription	Fetal Intestine Small	intestine
24	chr2:113058200-113090600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:113058800-113081800	Weak transcription	Fetal Lung	lung
26	chr2:113058800-113088800	Weak transcription	Dnd41	blood
27	chr2:113059000-113079000	Weak transcription	HSMM	muscle
28	chr2:113059000-113080200	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:113059000-113081800	Weak transcription	Thymus	Thymus
30	chr2:113059000-113088800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:113059200-113081600	Weak transcription	Brain Angular Gyrus	brain
32	chr2:113059200-113096800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:113059400-113080400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:113059600-113090000	Weak transcription	Colonic Mucosa	Colon
35	chr2:113060000-113084800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:113060000-113090600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:113060400-113090600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:113060800-113081800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:113061600-113081400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:113061600-113088800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:113062200-113084000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr2:113062200-113094400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:113062400-113074200	Weak transcription	Osteobl	bone
44	chr2:113062400-113081800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:113062400-113081800	Weak transcription	Brain Germinal Matrix	brain
46	chr2:113062400-113088800	Weak transcription	Aorta	Aorta
47	chr2:113062400-113090600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr2:113062800-113081400	Weak transcription	Small Intestine	intestine
49	chr2:113063000-113081600	Weak transcription	GM12878-XiMat	blood
50	chr2:113064600-113080600	Weak transcription	Brain Hippocampus Middle	brain

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