Variant report

Variant	rs9556711
Chromosome Location	chr13:98016416-98016417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:98016200-98016761	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr13:98014586-98016762	HepG2	liver:	n/a	n/a
3	POLR2A	chr13:98015961-98016610	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr13:98016250-98016425	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr13:98014322-98022665	K562	blood:	n/a	n/a

Variant related genes	Relation type
RNA5SP37	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11069259	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.86[EUR][1000 genomes]
rs11838553	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1556086	0.85[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap]
rs16954019	0.85[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap]
rs7333720	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7989284	0.85[CEU][hapmap]
rs9556703	0.81[CHB][hapmap]
rs9556709	0.91[ASN][1000 genomes]
rs9556710	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9584562	0.84[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832694	chr13:97930561-98137882	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1038798	chr13:98008467-98068130	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Alcoholism (alcohol use disorder factor score)	21529783	GWAS catalog
Alcoholism (alcohol dependence factor score)	21529783	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9556711	GPC6	cis	cerebellum	SCAN
rs9556711	GPC5	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:97982600-98020800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr13:97991600-98020800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr13:97992800-98020800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr13:97995400-98050200	Weak transcription	Small Intestine	intestine
5	chr13:97996200-98019400	Weak transcription	GM12878-XiMat	blood
6	chr13:97997400-98019000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr13:97999600-98019200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr13:98002400-98027200	Weak transcription	Lung	lung
9	chr13:98002400-98039600	Weak transcription	Spleen	Spleen
10	chr13:98002600-98021600	Weak transcription	Colonic Mucosa	Colon
11	chr13:98003200-98021200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr13:98003800-98018000	Weak transcription	Fetal Brain Male	brain
13	chr13:98003800-98019000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr13:98004000-98018600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr13:98004000-98019200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr13:98004000-98021000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr13:98004400-98019400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr13:98005400-98021600	Weak transcription	Thymus	Thymus
19	chr13:98006600-98020600	Strong transcription	HUVEC	blood vessel
20	chr13:98006800-98018600	Weak transcription	HSMMtube	muscle
21	chr13:98009200-98019200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr13:98009600-98019000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr13:98010000-98027400	Weak transcription	Esophagus	oesophagus
24	chr13:98010800-98027400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr13:98011600-98017400	Strong transcription	Primary hematopoietic stem cells	blood
26	chr13:98011800-98019200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr13:98011800-98020800	Weak transcription	Stomach Mucosa	stomach
28	chr13:98012000-98019400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr13:98012200-98020400	Strong transcription	Fetal Lung	lung
30	chr13:98012400-98019000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr13:98012600-98017200	Strong transcription	Fetal Muscle Trunk	muscle
32	chr13:98012600-98017400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr13:98012600-98017400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr13:98012800-98017400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr13:98012800-98018600	Strong transcription	Primary B cells from cord blood	blood
36	chr13:98012800-98019200	Strong transcription	Placenta	Placenta
37	chr13:98012800-98019200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr13:98012800-98019400	Strong transcription	Duodenum Mucosa	Duodenum
39	chr13:98012800-98020200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr13:98013000-98017400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr13:98013000-98017600	Strong transcription	Stomach Smooth Muscle	stomach
42	chr13:98013000-98018600	Strong transcription	Fetal Muscle Leg	muscle
43	chr13:98013000-98020200	Strong transcription	Primary T cells from cord blood	blood
44	chr13:98013400-98016600	Strong transcription	Fetal Intestine Large	intestine
45	chr13:98013400-98018600	Weak transcription	HMEC	breast
46	chr13:98013600-98017200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr13:98013600-98018000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr13:98013600-98019200	Weak transcription	Fetal Thymus	thymus
49	chr13:98013800-98021200	Weak transcription	NHEK	skin
50	chr13:98014000-98018400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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