Variant report

Variant	rs10757027
Chromosome Location	chr9:19124596-19124597
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:19115262..19117243-chr9:19122204..19125901,3	K562	blood:
2	chr9:19124177..19125684-chr9:19126025..19128795,2	MCF-7	breast:
3	chr9:19047700..19050673-chr9:19122479..19124686,3	K562	blood:

Variant related genes	Relation type
ENSG00000155876	Chromatin interaction
ENSG00000147872	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10811116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963972	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12338361	0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3808660	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7850966	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv430003	chr9:19074740-19247826	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv870340	chr9:19077714-19143230	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1018947	chr9:19094894-19394712	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
9	nsv1033552	chr9:19104662-19131866	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10757027	PLIN2	cis	lymphoblastoid	seeQTL
rs10757027	FAM154A	cis	cerebellum	SCAN
rs10757027	ADFP	cis	multi-tissue	Pritchard
rs10757027	PLIN2	cis	Lymphoblastoid	GTEx
rs10757027	ADFP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19103400-19126400	Weak transcription	Fetal Brain Male	brain
2	chr9:19110600-19126400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:19113400-19126200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:19114000-19124800	Strong transcription	Fetal Muscle Trunk	muscle
5	chr9:19114000-19126000	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr9:19114200-19124800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:19114200-19126200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:19114800-19124800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr9:19114800-19126000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:19114800-19126000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:19115000-19125200	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr9:19116000-19124600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:19116400-19127000	Weak transcription	Stomach Mucosa	stomach
14	chr9:19116600-19126000	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr9:19116600-19126000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:19116800-19124600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr9:19117000-19127000	Weak transcription	HSMMtube	muscle
18	chr9:19118000-19126600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:19118400-19126600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr9:19119600-19124800	Strong transcription	NHLF	lung
21	chr9:19120600-19126600	Weak transcription	Fetal Brain Female	brain
22	chr9:19121200-19125400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:19121200-19126000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:19121200-19126200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:19121200-19126400	Weak transcription	Brain Germinal Matrix	brain
26	chr9:19121200-19127000	Weak transcription	Brain Angular Gyrus	brain
27	chr9:19121400-19125400	Weak transcription	Pancreas	Pancrea
28	chr9:19121400-19126200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr9:19121400-19127000	Weak transcription	Brain Anterior Caudate	brain
30	chr9:19121600-19126600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr9:19121800-19125200	Weak transcription	Gastric	stomach
32	chr9:19121800-19126000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr9:19121800-19127000	Weak transcription	Aorta	Aorta
34	chr9:19122400-19126000	Weak transcription	Hela-S3	cervix
35	chr9:19122400-19126400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:19122600-19125200	Genic enhancers	Left Ventricle	heart
37	chr9:19122800-19126400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:19123000-19125200	Weak transcription	Lung	lung
39	chr9:19123000-19126000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr9:19123000-19126000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr9:19123000-19126000	Weak transcription	Colonic Mucosa	Colon
42	chr9:19123000-19126200	Transcr. at gene 5' and 3'	HepG2	liver
43	chr9:19123000-19126400	Weak transcription	Brain Hippocampus Middle	brain
44	chr9:19123000-19127000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr9:19123200-19126200	Weak transcription	Colon Smooth Muscle	Colon
46	chr9:19123400-19124600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr9:19123400-19124600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:19123400-19124800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr9:19123400-19125600	Enhancers	Fetal Heart	heart
50	chr9:19123400-19126000	Genic enhancers	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links