Variant report

Variant	rs7570679
Chromosome Location	chr2:113252998-113252999
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113252098..113253969-chr2:113305095..113307068,2	MCF-7	breast:
2	chr2:113238650..113242491-chr2:113249319..113253275,7	MCF-7	breast:
3	chr2:113249787..113252552-chr2:113252556..113255186,2	K562	blood:

Variant related genes	Relation type
ENSG00000114999	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11679929	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12987434	1.00[ASN][1000 genomes]
rs12988536	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989407	1.00[ASN][1000 genomes]
rs13025468	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[ASN][1000 genomes]
rs1465817	0.93[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561266	0.86[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34047777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34263686	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34364366	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34892661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36086865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3961916	0.93[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158651	1.00[ASN][1000 genomes]
rs6707618	1.00[CEU][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs6708841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708927	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67178025	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726169	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729910	0.85[CEU][hapmap];0.91[GIH][hapmap]
rs6757757	0.85[CEU][hapmap]
rs6759275	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[ASN][1000 genomes]
rs71414672	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71414673	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573493	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586685	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589793	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7570679	RGPD8	cis	Thyroid	GTEx
rs7570679	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs7570679	RGPD8	cis	Artery Tibial	GTEx
rs7570679	RGPD8	cis	Esophagus Muscularis	GTEx
rs7570679	RGPD8	cis	Esophagus Mucosa	GTEx
rs7570679	RGPD8	cis	Adipose Subcutaneous	GTEx
rs7570679	RGPD8	cis	Nerve Tibial	GTEx
rs7570679	RGPD8	cis	lung	GTEx
rs7570679	RGPD8	cis	Artery Aorta	GTEx
rs7570679	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs7570679	RGPD8	cis	Whole Blood	GTEx
rs7570679	RGPD8	cis	Muscle Skeletal	GTEx
rs7570679	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113241000-113277200	Weak transcription	Gastric	stomach
2	chr2:113241000-113277800	Weak transcription	Colonic Mucosa	Colon
3	chr2:113241200-113259600	Weak transcription	Esophagus	oesophagus
4	chr2:113241200-113271600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:113241200-113277800	Weak transcription	Pancreas	Pancrea
6	chr2:113241200-113278000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:113241200-113286400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:113241400-113254000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:113241400-113279200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:113241600-113260600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:113241600-113277200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:113241600-113292400	Weak transcription	Small Intestine	intestine
13	chr2:113241800-113257800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:113241800-113286000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:113241800-113286200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:113242000-113259600	Weak transcription	Fetal Heart	heart
17	chr2:113242400-113255600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr2:113244200-113254200	Strong transcription	Dnd41	blood
19	chr2:113244800-113259600	Weak transcription	GM12878-XiMat	blood
20	chr2:113245800-113277200	Weak transcription	Right Ventricle	heart
21	chr2:113245800-113277200	Weak transcription	Spleen	Spleen
22	chr2:113246200-113271600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:113250400-113253800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:113250600-113256200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:113250800-113253800	Strong transcription	Stomach Smooth Muscle	stomach
26	chr2:113250800-113254600	Strong transcription	Fetal Thymus	thymus
27	chr2:113251000-113253200	Strong transcription	Brain Germinal Matrix	brain
28	chr2:113251000-113254200	Strong transcription	Fetal Brain Female	brain
29	chr2:113251400-113253000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr2:113251400-113253200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:113251400-113253400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:113251400-113253600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr2:113251400-113253800	Strong transcription	Fetal Stomach	stomach
34	chr2:113251400-113254200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr2:113251600-113253000	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:113251600-113253000	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:113251600-113253200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:113251600-113253200	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:113251600-113253200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:113251600-113253200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr2:113251600-113253200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr2:113251600-113253200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:113251600-113253200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:113251600-113253200	Strong transcription	Fetal Brain Male	brain
45	chr2:113251600-113253400	Strong transcription	Thymus	Thymus
46	chr2:113251600-113253600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:113251600-113253600	Strong transcription	Primary B cells from cord blood	blood
48	chr2:113251600-113253600	Strong transcription	Primary T cells from cord blood	blood
49	chr2:113251600-113253600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:113251600-113253800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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