Variant report

Variant	rs7569407
Chromosome Location	chr2:113251000-113251001
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:112812787..112814329-chr2:113250913..113252754,2	MCF-7	breast:
2	chr2:113238453..113240816-chr2:113250907..113252932,2	K562	blood:
3	chr2:112988264..112989991-chr2:113249317..113251207,2	K562	blood:
4	chr2:113249787..113252523-chr2:113253686..113256564,2	K562	blood:
5	chr2:113238650..113242491-chr2:113249319..113253275,7	MCF-7	breast:
6	chr2:113244108..113246040-chr2:113250094..113252962,3	MCF-7	breast:
7	chr2:113239379..113240948-chr2:113249251..113251583,2	MCF-7	breast:
8	chr2:113244367..113247347-chr2:113249127..113251092,3	MCF-7	breast:
9	chr2:113249787..113252552-chr2:113252556..113255186,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000114999	Chromatin interaction
ENSG00000153214	Chromatin interaction
ENSG00000144161	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10153558	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10153801	0.92[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs11123137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1127264	0.92[ASN][1000 genomes]
rs11644	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs11899598	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12465241	0.92[ASN][1000 genomes]
rs12465446	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13030618	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1437673	0.84[CEU][hapmap]
rs1437675	0.88[CEU][hapmap];0.83[CHB][hapmap];0.81[TSI][hapmap]
rs1545133	0.84[CEU][hapmap]
rs17043158	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17043167	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28542310	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34082454	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35419160	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3849314	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3910512	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4849073	0.84[CEU][hapmap]
rs4849074	0.84[CEU][hapmap]
rs56010201	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62157527	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6542059	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542060	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542061	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6717635	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6718241	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6718489	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs6760014	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7580213	0.84[EUR][1000 genomes];0.89[ASN][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7569407	POLR1B	cis	parietal	SCAN
rs7569407	FBLN7	cis	parietal	SCAN
rs7569407	RGPD8	cis	Artery Tibial	GTEx
rs7569407	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs7569407	RGPD8	cis	Nerve Tibial	GTEx
rs7569407	RGPD8	cis	Adipose Subcutaneous	GTEx
rs7569407	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs7569407	POLR1B	cis	cerebellum	SCAN
rs7569407	RGPD8	cis	lung	GTEx
rs7569407	RGPD8	cis	Muscle Skeletal	GTEx
rs7569407	TTL	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:140 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113240800-113251600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:113241000-113251600	Weak transcription	Aorta	Aorta
3	chr2:113241000-113277200	Weak transcription	Gastric	stomach
4	chr2:113241000-113277800	Weak transcription	Colonic Mucosa	Colon
5	chr2:113241200-113251000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:113241200-113251600	Weak transcription	Placenta	Placenta
7	chr2:113241200-113251800	Weak transcription	Left Ventricle	heart
8	chr2:113241200-113251800	Weak transcription	Psoas Muscle	Psoas
9	chr2:113241200-113252200	Weak transcription	Ovary	ovary
10	chr2:113241200-113259600	Weak transcription	Esophagus	oesophagus
11	chr2:113241200-113271600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:113241200-113277800	Weak transcription	Pancreas	Pancrea
13	chr2:113241200-113278000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:113241200-113286400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:113241400-113251000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:113241400-113251600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:113241400-113251800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:113241400-113252000	Weak transcription	Fetal Kidney	kidney
19	chr2:113241400-113254000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr2:113241400-113279200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:113241600-113251600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr2:113241600-113251600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:113241600-113251600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:113241600-113251800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:113241600-113252000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:113241600-113252600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:113241600-113260600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:113241600-113277200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:113241600-113292400	Weak transcription	Small Intestine	intestine
30	chr2:113241800-113251000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:113241800-113251000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:113241800-113251400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:113241800-113251400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:113241800-113251600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr2:113241800-113251600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:113241800-113251800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr2:113241800-113251800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:113241800-113252000	Weak transcription	Liver	Liver
39	chr2:113241800-113252000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:113241800-113257800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:113241800-113286000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:113241800-113286200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr2:113242000-113251400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:113242000-113259600	Weak transcription	Fetal Heart	heart
45	chr2:113242400-113251000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr2:113242400-113251600	Weak transcription	Fetal Brain Male	brain
47	chr2:113242400-113251800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:113242400-113252200	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:113242400-113252400	Weak transcription	Fetal Lung	lung
50	chr2:113242400-113255600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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