Variant report

Variant	rs1873676
Chromosome Location	chr12:31463873-31463874
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	GATA2	chr12:31463688-31463998	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr12:31462633-31466037	K562	blood:	n/a	n/a
3	POLR2A	chr12:31463709-31465704	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:31463823-31464006	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:31461939-31465879	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr12:31463667-31463929	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000256176	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13328978	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57445509	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57566796	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7307202	0.85[ASN][1000 genomes]
rs7310096	0.92[ASN][1000 genomes]
rs7958150	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS 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	71 gene(s)	inside rSNPs	diseases
3	esv2758303	chr12:31125467-31491104	Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	esv2759890	chr12:31125467-31491104	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv428276	chr12:31125467-31491104	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
6	esv2751043	chr12:31148662-31499671	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	esv2751053	chr12:31225710-31484881	Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	esv2754121	chr12:31225710-31493435	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	esv2751054	chr12:31225710-31513718	Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers 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	47 gene(s)	inside rSNPs	diseases
11	esv35092	chr12:31239600-31484833	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
12	esv2751071	chr12:31239600-31493435	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
13	esv2751072	chr12:31239600-31499671	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
14	nsv430477	chr12:31239600-31513718	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS 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	42 gene(s)	inside rSNPs	diseases
15	esv2751077	chr12:31278031-31499671	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
16	nsv524737	chr12:31399901-31464663	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31428600-31470000	Weak transcription	Small Intestine	intestine
2	chr12:31433000-31470200	Weak transcription	Stomach Mucosa	stomach
3	chr12:31440800-31470000	Weak transcription	Fetal Lung	lung
4	chr12:31446600-31468000	Weak transcription	Fetal Heart	heart
5	chr12:31446600-31470000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr12:31448000-31468000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:31449800-31464000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:31449800-31472800	Weak transcription	Pancreas	Pancrea
9	chr12:31450000-31464000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:31450000-31471000	Weak transcription	Esophagus	oesophagus
11	chr12:31451000-31470400	Weak transcription	Colonic Mucosa	Colon
12	chr12:31455200-31469800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:31457000-31467600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr12:31457200-31467800	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:31457200-31469800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:31457400-31465800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:31457600-31467800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:31457600-31475800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:31457800-31470200	Weak transcription	Adipose Nuclei	Adipose
20	chr12:31458000-31469800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:31458000-31470600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:31458000-31471000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:31458200-31467600	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr12:31458200-31467800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr12:31458200-31468000	Weak transcription	Fetal Kidney	kidney
26	chr12:31458200-31470000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr12:31458200-31470200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:31458200-31470400	Weak transcription	Liver	Liver
29	chr12:31458200-31470600	Weak transcription	HSMMtube	muscle
30	chr12:31458400-31466800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:31458400-31467600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr12:31458400-31467600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr12:31458400-31467600	Weak transcription	Ovary	ovary
34	chr12:31458400-31467800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:31458400-31468200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:31458400-31469600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:31458400-31469800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:31458400-31469800	Weak transcription	HSMM	muscle
39	chr12:31458400-31470000	Weak transcription	Thymus	Thymus
40	chr12:31458400-31470400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:31458400-31470400	Weak transcription	Fetal Stomach	stomach
42	chr12:31458400-31470600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:31458600-31466800	Weak transcription	Fetal Intestine Small	intestine
44	chr12:31458600-31468000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:31458800-31467600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr12:31458800-31468400	Weak transcription	Fetal Intestine Large	intestine
47	chr12:31459400-31467800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:31459800-31467800	Weak transcription	HUVEC	blood vessel
49	chr12:31459800-31470200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:31460000-31467600	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links