Variant report

Variant	rs12887734
Chromosome Location	chr14:104046834-104046835
allele	G/T
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	chr14:104046711-104046869	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000264904	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10431750	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11844466	0.86[AMR][1000 genomes]
rs11851000	0.86[AMR][1000 genomes]
rs11851616	0.86[AMR][1000 genomes]
rs12889403	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12889721	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12889731	0.84[AMR][1000 genomes]
rs12890820	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12892038	0.86[AMR][1000 genomes]
rs12894729	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274267	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296482	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2403196	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2403197	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2896487	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34026011	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34186780	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34843146	0.84[AMR][1000 genomes]
rs34896432	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35026580	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35229468	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35496194	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35498576	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4525427	0.84[AMR][1000 genomes]
rs4906335	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4906336	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4906337	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4906338	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4906347	0.80[AMR][1000 genomes]
rs55751606	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57072546	0.87[AMR][1000 genomes]
rs58033365	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60249782	0.87[AMR][1000 genomes]
rs67899457	0.85[AMR][1000 genomes]
rs7140568	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71417868	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71417869	0.80[AMR][1000 genomes]
rs7148456	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs729438	0.80[AMR][1000 genomes]
rs8017628	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8017993	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv832883	chr14:103927687-104120953	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv902297	chr14:103956182-104061646	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902298	chr14:103959289-104061646	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	43 gene(s)	inside rSNPs	diseases
5	nsv902299	chr14:103967504-104061646	Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
7	nsv902304	chr14:103979953-104061646	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv902305	chr14:103979953-104073551	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	nsv566022	chr14:104007555-104092789	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	25056061	GWAS catalog

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104030800-104073200	Weak transcription	Small Intestine	intestine
2	chr14:104035400-104060400	Weak transcription	Fetal Brain Male	brain
3	chr14:104037400-104048400	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr14:104038400-104048800	Strong transcription	Fetal Brain Female	brain
5	chr14:104038400-104049400	Strong transcription	Primary T cells from cord blood	blood
6	chr14:104038800-104051000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr14:104041000-104059600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr14:104041000-104063200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr14:104041600-104056200	Weak transcription	K562	blood
10	chr14:104041600-104056400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr14:104041800-104052600	Weak transcription	Psoas Muscle	Psoas
12	chr14:104041800-104059600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr14:104041800-104060600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr14:104042200-104057200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr14:104043400-104049200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr14:104043400-104051200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr14:104043400-104051200	Strong transcription	Fetal Intestine Large	intestine
18	chr14:104043400-104052000	Strong transcription	Fetal Intestine Small	intestine
19	chr14:104043400-104056600	Weak transcription	Fetal Heart	heart
20	chr14:104043600-104048000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr14:104043600-104048400	Strong transcription	HSMM	muscle
22	chr14:104043800-104047600	Weak transcription	Brain Substantia Nigra	brain
23	chr14:104043800-104047600	Weak transcription	Right Ventricle	heart
24	chr14:104043800-104049200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr14:104043800-104050800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr14:104043800-104051400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr14:104043800-104051600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr14:104043800-104051600	Strong transcription	Fetal Muscle Leg	muscle
29	chr14:104043800-104055400	Weak transcription	Brain Angular Gyrus	brain
30	chr14:104043800-104058200	Strong transcription	Fetal Stomach	stomach
31	chr14:104043800-104059600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr14:104043800-104060200	Weak transcription	Stomach Mucosa	stomach
33	chr14:104044000-104047400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr14:104044000-104047400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr14:104044000-104047600	Weak transcription	HMEC	breast
36	chr14:104044000-104048000	Weak transcription	NHEK	skin
37	chr14:104044000-104049000	Strong transcription	Brain Germinal Matrix	brain
38	chr14:104044000-104055000	Weak transcription	Colon Smooth Muscle	Colon
39	chr14:104044000-104056600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr14:104044400-104048200	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr14:104044600-104048800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr14:104044600-104049000	Strong transcription	Adipose Nuclei	Adipose
43	chr14:104044600-104049200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr14:104044600-104051000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr14:104045000-104047600	Weak transcription	NH-A	brain
46	chr14:104045000-104048400	Strong transcription	Liver	Liver
47	chr14:104045000-104049000	Strong transcription	Pancreas	Pancrea
48	chr14:104045200-104048800	Strong transcription	Lung	lung
49	chr14:104045200-104049200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr14:104045200-104050000	Weak transcription	HSMMtube	muscle

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