Variant report

Variant	rs7599551
Chromosome Location	chr2:112973924-112973925
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:112973461..112975614-chr2:113086983..113088947,2	K562	blood:
2	chr2:112951584..112954531-chr2:112972877..112975539,2	MCF-7	breast:
3	chr2:112962920..112964823-chr2:112973839..112975867,2	K562	blood:
4	chr2:112973488..112974403-chr2:113238331..113238853,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 15 )

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

rs_ID	r²[population]
rs10864901	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11123133	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11676628	0.85[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11679986	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11682795	0.93[CEU][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11685462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11685514	0.93[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11687980	0.93[CEU][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11688511	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11689858	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11691239	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11693294	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11695974	0.93[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12474447	0.93[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12477879	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4516428	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55798617	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55802705	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55821286	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55861985	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56044884	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56048537	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6711180	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6722612	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6747639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6759283	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6761440	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72831633	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72831634	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72831636	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72831638	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72831639	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72831641	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72831642	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72831649	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831651	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831658	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831660	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831662	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72831664	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72831685	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72831688	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72833410	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72833412	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72833413	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72833414	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72833415	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72833428	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72833431	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72833432	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7586893	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7587316	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7596661	0.93[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7599551	RGPD8	cis	Esophagus Muscularis	GTEx
rs7599551	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs7599551	RGPD8	cis	Whole Blood	GTEx
rs7599551	RGPD8	cis	Artery Tibial	GTEx
rs7599551	RGPD8	cis	Heart Left Ventricle	GTEx
rs7599551	RGPD8	cis	Artery Aorta	GTEx
rs7599551	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs7599551	RGPD8	cis	Muscle Skeletal	GTEx
rs7599551	RGPD8	cis	Thyroid	GTEx
rs7599551	RGPD8	cis	Adipose Subcutaneous	GTEx
rs7599551	RGPD8	cis	lung	GTEx
rs7599551	ZC3H8	cis	Artery Tibial	GTEx
rs7599551	RGPD8	cis	Esophagus Mucosa	GTEx
rs7599551	RGPD8	cis	Nerve Tibial	GTEx
rs7599551	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112959600-112987000	Weak transcription	Osteobl	bone
2	chr2:112961000-113009000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:112962400-112979000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr2:112963200-112978800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:112967600-112977000	Weak transcription	Fetal Kidney	kidney
6	chr2:112967800-112977600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:112967800-112978000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:112967800-112986600	Weak transcription	NHEK	skin
9	chr2:112967800-112987000	Weak transcription	Aorta	Aorta
10	chr2:112968000-113011800	Weak transcription	Right Ventricle	heart
11	chr2:112968200-112978800	Weak transcription	Fetal Lung	lung
12	chr2:112968200-112979600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:112968200-112999000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:112968200-113004000	Weak transcription	Fetal Brain Male	brain
15	chr2:112968200-113009200	Weak transcription	Small Intestine	intestine
16	chr2:112968200-113012000	Weak transcription	Pancreas	Pancrea
17	chr2:112968400-112978800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:112968400-112981400	Weak transcription	K562	blood
19	chr2:112968400-112986800	Weak transcription	NHDF-Ad	bronchial
20	chr2:112968400-113003800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:112968600-112977800	Weak transcription	Placenta	Placenta
22	chr2:112968800-112977000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:112968800-113011400	Weak transcription	Brain Angular Gyrus	brain
24	chr2:112968800-113011800	Weak transcription	Brain Substantia Nigra	brain
25	chr2:112969000-112975000	Weak transcription	Fetal Heart	heart
26	chr2:112969000-112993000	Weak transcription	Colonic Mucosa	Colon
27	chr2:112969000-113005200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:112969200-112975200	Weak transcription	HSMMtube	muscle
29	chr2:112969200-112992000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:112969400-112974200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:112969400-113011800	Weak transcription	Esophagus	oesophagus
32	chr2:112969600-112974000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:112969600-112974000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:112969600-112974000	Strong transcription	Fetal Thymus	thymus
35	chr2:112969600-113009000	Weak transcription	Psoas Muscle	Psoas
36	chr2:112969800-112974000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:112969800-112977800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:112970000-112974000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:112970000-112977800	Weak transcription	Fetal Intestine Small	intestine
40	chr2:112970200-112987600	Weak transcription	Adipose Nuclei	Adipose
41	chr2:112970200-112992600	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:112970200-113004800	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:112970400-112974200	Strong transcription	Dnd41	blood
44	chr2:112970600-112978000	Weak transcription	Thymus	Thymus
45	chr2:112970600-112978400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:112970600-112982400	Weak transcription	NHLF	lung
47	chr2:112970800-112974000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:112970800-112977600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:112970800-112979800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr2:112970800-113003800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links