Variant report

Variant	rs7125
Chromosome Location	chr19:18288069-18288070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18286313..18288338-chr19:18390930..18393715,2	K562	blood:
2	chr19:18287723..18291034-chr19:18291646..18293887,3	K562	blood:
3	chr19:18283035..18288338-chr19:18301660..18307351,8	K562	blood:
4	chr19:18282590..18284654-chr19:18287591..18290357,2	K562	blood:
5	chr19:18272224..18273796-chr19:18288060..18290729,2	K562	blood:
6	chr19:18282952..18288338-chr19:18301660..18306832,7	K562	blood:
7	chr19:18285361..18288338-chr19:18390930..18392881,2	K562	blood:

Variant related genes	Relation type
ENSG00000216490	Chromatin interaction
ENSG00000254858	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000267959	Chromatin interaction
ENSG00000105647	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11668048	0.86[YRI][hapmap]
rs1566029	0.81[JPT][hapmap]
rs16982263	0.87[LWK][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap]
rs200373	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200378	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200380	0.94[ASN][1000 genomes]
rs200383	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2267922	0.81[JPT][hapmap]
rs3736328	0.81[JPT][hapmap]
rs4808759	0.85[CHB][hapmap];0.97[CHD][hapmap];0.88[LWK][hapmap];0.84[MKK][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
5	nsv833773	chr19:18152971-18302988	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv911241	chr19:18193191-18304700	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv911242	chr19:18201757-18304700	Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv911244	chr19:18206681-18304700	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv911245	chr19:18206681-18338101	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv833774	chr19:18213761-18295329	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
12	nsv911247	chr19:18224729-18288069	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv911248	chr19:18224729-18338101	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
14	nsv911249	chr19:18224729-18375846	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
15	nsv911250	chr19:18224729-18376522	Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
16	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
17	nsv911252	chr19:18234588-18338101	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
18	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
19	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
20	nsv911254	chr19:18248146-18310678	Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
21	nsv911256	chr19:18255359-18338101	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
22	nsv911260	chr19:18288069-18386798	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7125	PIK3R2	cis	cerebellum	SCAN
rs7125	TM6SF2	cis	cerebellum	SCAN
rs7125	GMIP	cis	cerebellum	SCAN
rs7125	HSH2D	cis	cerebellum	SCAN
rs7125	HAPLN4	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18285000-18290200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
2	chr19:18285200-18288400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:18285200-18288800	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
4	chr19:18285200-18289600	Weak transcription	Small Intestine	intestine
5	chr19:18285400-18296200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:18285600-18289000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr19:18285600-18291800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr19:18286000-18290200	Weak transcription	Osteobl	bone
9	chr19:18286000-18291200	Weak transcription	Brain Hippocampus Middle	brain
10	chr19:18286200-18288800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:18286200-18290600	Weak transcription	Pancreas	Pancrea
12	chr19:18286200-18290800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:18286200-18292200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr19:18286200-18292400	Weak transcription	Colon Smooth Muscle	Colon
15	chr19:18286200-18294200	Weak transcription	Stomach Mucosa	stomach
16	chr19:18286400-18288800	Genic enhancers	Spleen	Spleen
17	chr19:18286400-18290400	Genic enhancers	Primary B cells from peripheral blood	blood
18	chr19:18286400-18296200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr19:18286600-18288800	Strong transcription	Lung	lung
20	chr19:18286600-18289000	Genic enhancers	Primary B cells from cord blood	blood
21	chr19:18286600-18289400	Weak transcription	Esophagus	oesophagus
22	chr19:18286600-18289400	Strong transcription	Gastric	stomach
23	chr19:18286600-18290400	Strong transcription	Fetal Intestine Small	intestine
24	chr19:18286600-18290800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr19:18286600-18294200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr19:18286600-18296200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr19:18286600-18296200	Weak transcription	K562	blood
28	chr19:18286600-18296400	Weak transcription	HepG2	liver
29	chr19:18286600-18302600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:18287200-18288400	Strong transcription	Liver	Liver
31	chr19:18287200-18288400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
32	chr19:18287200-18288800	Genic enhancers	Placenta	Placenta
33	chr19:18287200-18289400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:18287400-18289200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr19:18287400-18289400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr19:18287600-18289200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr19:18287800-18288200	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr19:18287800-18288600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
39	chr19:18287800-18289200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:18287800-18290000	Strong transcription	Fetal Intestine Large	intestine
41	chr19:18287800-18290200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:18287800-18293000	Weak transcription	Hela-S3	cervix
43	chr19:18287800-18295000	Weak transcription	Colonic Mucosa	Colon
44	chr19:18288000-18288800	Strong transcription	Adipose Nuclei	Adipose
45	chr19:18288000-18290000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr19:18288000-18296400	Weak transcription	H9 Cell Line	embryonic stem cell

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