Variant report

Variant	rs12672257
Chromosome Location	chr7:19813466-19813467
allele	C/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	CTCF	chr7:19813320-19813470	HRPEpiC	eye:	n/a	n/a
2	TAF1	chr7:19812670-19813597	H1-neurons	neurons:	n/a	n/a
3	CTCF	chr7:19813320-19813470	HAc	cerebellar:	n/a	n/a
4	CREB1	chr7:19812810-19813571	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr7:19811640-19813510	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr7:19811609-19813496	H1-neurons	neurons:	n/a	n/a
7	CREB1	chr7:19812837-19813489	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTBP2	chr7:19812282-19813636	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr7:19813413-19813482	A549	lung:	n/a	n/a
10	SIN3A	chr7:19811749-19813519	H1-hESC	embryonic stem cell:	n/a	chr7:19812659-19812672 chr7:19812664-19812678 chr7:19813152-19813165 chr7:19812656-19812665
11	REST	chr7:19811647-19813838	H1-neurons	neurons:	n/a	chr7:19812911-19812931 chr7:19812659-19812668 chr7:19812911-19812925 chr7:19812509-19812517 chr7:19812659-19812679 chr7:19813152-19813165 chr7:19812913-19812923

Variant related genes	Relation type
TMEM196	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10228783	0.93[EUR][1000 genomes]
rs10231980	0.93[EUR][1000 genomes]
rs10232870	1.00[CEU][hapmap]
rs10239147	0.90[EUR][1000 genomes]
rs10243965	0.93[EUR][1000 genomes]
rs10249477	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10249635	0.93[EUR][1000 genomes]
rs10251774	0.93[EUR][1000 genomes]
rs10252597	0.93[EUR][1000 genomes]
rs10252965	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10260866	0.93[EUR][1000 genomes]
rs10267417	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10269891	1.00[CEU][hapmap]
rs10270468	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10276518	0.90[EUR][1000 genomes]
rs10486365	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12113916	0.90[EUR][1000 genomes]
rs12334001	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12334267	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12386623	0.93[EUR][1000 genomes]
rs12666488	0.93[EUR][1000 genomes]
rs12672320	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12673842	0.85[CEU][hapmap]
rs12700075	0.93[EUR][1000 genomes]
rs12700077	0.93[EUR][1000 genomes]
rs1468287	0.93[EUR][1000 genomes]
rs17141882	0.93[EUR][1000 genomes]
rs17141884	0.93[EUR][1000 genomes]
rs17141945	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2189570	0.93[EUR][1000 genomes]
rs2390156	0.93[EUR][1000 genomes]
rs2390157	0.93[EUR][1000 genomes]
rs28537170	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28605851	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4719587	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4721824	0.93[EUR][1000 genomes]
rs61670426	0.93[EUR][1000 genomes]
rs6945297	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6945533	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6945753	0.86[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7798760	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7812001	0.86[CHB][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018601	chr7:19272360-20008881	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1033223	chr7:19682192-20461375	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv538795	chr7:19682192-20461375	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv830918	chr7:19747674-19914527	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	esv1847477	chr7:19778086-19970584	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:19809600-19813600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr7:19811400-19813600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
3	chr7:19811600-19813600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr7:19811800-19813600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr7:19811800-19813600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr7:19811800-19813600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:19812000-19813600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr7:19812000-19813600	Enhancers	Ovary	ovary
9	chr7:19812000-19813600	Enhancers	Pancreas	Pancrea
10	chr7:19812200-19813600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:19812400-19813600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr7:19812600-19813600	Active TSS	Brain Anterior Caudate	brain
13	chr7:19812600-19813600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
14	chr7:19812600-19813600	Enhancers	Gastric	stomach
15	chr7:19813000-19813600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:19813000-19813600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr7:19813000-19813600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:19813200-19813600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr7:19813200-19813600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:19813200-19813600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
21	chr7:19813200-19813600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:19813200-19813600	Flanking Active TSS	Brain Germinal Matrix	brain
23	chr7:19813200-19813600	Enhancers	Fetal Brain Male	brain
24	chr7:19813200-19813600	Bivalent Enhancer	Fetal Intestine Small	intestine
25	chr7:19813200-19813600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr7:19813200-19813600	Bivalent Enhancer	Right Atrium	heart
27	chr7:19813200-19813600	Bivalent/Poised TSS	NHEK	skin
28	chr7:19813400-19813600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
29	chr7:19813400-19813600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr7:19813400-19813600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:19813400-19813600	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
32	chr7:19813400-19813600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr7:19813400-19813600	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr7:19813400-19813600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
35	chr7:19813400-19813600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
36	chr7:19813400-19813600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
37	chr7:19813400-19813600	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr7:19813400-19813600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr7:19813400-19813600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:19813400-19813600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
41	chr7:19813400-19813600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
42	chr7:19813400-19813600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
43	chr7:19813400-19813600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr7:19813400-19813600	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
45	chr7:19813400-19813600	Flanking Active TSS	Fetal Brain Female	brain
46	chr7:19813400-19813600	Bivalent Enhancer	Fetal Muscle Leg	muscle
47	chr7:19813400-19813600	Bivalent Enhancer	Left Ventricle	heart
48	chr7:19813400-19813600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links