Variant report

Variant	rs7019027
Chromosome Location	chr9:7051826-7051827
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:7051581..7054293-chr9:7055466..7057984,2	MCF-7	breast:
2	chr9:7046839..7049487-chr9:7050524..7052607,2	K562	blood:

Variant related genes	Relation type
ENSG00000107077	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1407856	0.94[CEU][hapmap];0.86[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16925220	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16925247	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16925266	0.94[CEU][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs16925288	0.93[CEU][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs16925292	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs17511776	1.00[YRI][hapmap]
rs4740869	1.00[CEU][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs4742299	0.94[CEU][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs55754223	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56348300	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61075062	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62533860	0.90[EUR][1000 genomes]
rs62533862	0.92[EUR][1000 genomes]
rs62533897	0.87[EUR][1000 genomes]
rs62534415	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62534428	0.85[AMR][1000 genomes]
rs62534433	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62534435	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62534436	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62536962	0.80[EUR][1000 genomes]
rs73639964	0.90[EUR][1000 genomes]
rs73639965	0.90[EUR][1000 genomes]
rs7866711	0.94[CEU][hapmap];0.95[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7867935	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv892181	chr9:6680477-7070962	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking 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	70 gene(s)	inside rSNPs	diseases
3	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv831501	chr9:6868099-7058526	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv892185	chr9:6929053-7070962	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv870178	chr9:6941584-7060029	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv892186	chr9:6942605-7075305	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1024763	chr9:7022554-7061314	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv466117	chr9:7030268-7084558	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv613258	chr9:7030268-7084558	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv613259	chr9:7032776-7541338	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv1015874	chr9:7048807-7434890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
13	nsv539971	chr9:7048807-7434890	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7019027	PPAPDC2	cis	parietal	SCAN
rs7019027	INSL6	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7009000-7055200	Weak transcription	K562	blood
2	chr9:7009000-7056400	Weak transcription	Brain Substantia Nigra	brain
3	chr9:7009000-7076600	Weak transcription	HSMM	muscle
4	chr9:7009200-7077600	Weak transcription	Osteobl	bone
5	chr9:7009800-7076600	Weak transcription	HSMMtube	muscle
6	chr9:7012200-7052600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:7012200-7111200	Weak transcription	Colonic Mucosa	Colon
8	chr9:7012800-7076800	Weak transcription	Pancreas	Pancrea
9	chr9:7017800-7075000	Weak transcription	HepG2	liver
10	chr9:7018800-7064400	Weak transcription	Psoas Muscle	Psoas
11	chr9:7020000-7052800	Weak transcription	NHLF	lung
12	chr9:7028400-7052800	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:7028400-7076800	Weak transcription	Placenta	Placenta
14	chr9:7028800-7076400	Weak transcription	Aorta	Aorta
15	chr9:7028800-7077000	Weak transcription	Esophagus	oesophagus
16	chr9:7028800-7086400	Weak transcription	Right Ventricle	heart
17	chr9:7029000-7052600	Weak transcription	Brain Anterior Caudate	brain
18	chr9:7029000-7061400	Weak transcription	Fetal Intestine Small	intestine
19	chr9:7029000-7076400	Weak transcription	Ovary	ovary
20	chr9:7029000-7076600	Weak transcription	Lung	lung
21	chr9:7029000-7077400	Weak transcription	Gastric	stomach
22	chr9:7029000-7081200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:7034000-7103600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr9:7037200-7052800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr9:7041800-7052000	Strong transcription	Primary B cells from peripheral blood	blood
26	chr9:7042200-7056800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:7042800-7052400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:7043000-7069400	Weak transcription	NHDF-Ad	bronchial
29	chr9:7043400-7103600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr9:7044400-7052800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr9:7044400-7055600	Weak transcription	Hela-S3	cervix
32	chr9:7044800-7052600	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr9:7045000-7059200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr9:7045200-7052800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr9:7045400-7054600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:7045400-7077000	Weak transcription	Fetal Muscle Leg	muscle
37	chr9:7045400-7077000	Weak transcription	HMEC	breast
38	chr9:7045600-7055400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr9:7045800-7052800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr9:7046000-7052400	Weak transcription	Stomach Mucosa	stomach
41	chr9:7046000-7053400	Strong transcription	Primary B cells from cord blood	blood
42	chr9:7046200-7052000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr9:7046200-7052800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr9:7046200-7053600	Strong transcription	Primary T cells from cord blood	blood
45	chr9:7046400-7052000	Strong transcription	Adipose Nuclei	Adipose
46	chr9:7046400-7052000	Strong transcription	Thymus	Thymus
47	chr9:7046400-7052200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr9:7046400-7052600	Strong transcription	Fetal Thymus	thymus
49	chr9:7046400-7053000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr9:7046400-7077000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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