Variant report

Variant	rs6728741
Chromosome Location	chr2:50575299-50575300
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	REST	chr2:50569977-50575623	H1-neurons	neurons:	n/a	chr2:50573474-50573487 chr2:50573612-50573625 chr2:50570405-50570415 chr2:50574682-50574695 chr2:50574337-50574355
2	MXI1	chr2:50574069-50575390	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr2:50572819-50575367	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr2:50572889-50575342	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
NRXN1	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10182151	0.81[CEU][hapmap]
rs10191436	0.92[CEU][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs10865246	0.86[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs11125300	0.92[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs11125301	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs12465806	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12622261	0.92[CEU][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs13382330	0.82[CEU][hapmap]
rs13394447	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1402122	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1402126	0.92[CEU][hapmap]
rs1402128	0.82[CEU][hapmap]
rs1402129	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs1402167	0.85[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs1520435	0.86[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs1520450	0.89[CEU][hapmap]
rs1520452	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1520453	0.92[CEU][hapmap]
rs1818713	0.92[CEU][hapmap]
rs1829534	0.89[CEU][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs1851014	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1915174	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1949569	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2037387	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs2139628	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2160444	0.89[GIH][hapmap]
rs4318425	0.89[CEU][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs4377361	0.82[CEU][hapmap]
rs4971669	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4971675	0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs6545167	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6545169	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6722443	0.92[CEU][hapmap]
rs6728836	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559624	0.89[CEU][hapmap]
rs7574552	0.92[CEU][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs7577661	0.92[CEU][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs7587241	0.96[CEU][hapmap];0.92[YRI][hapmap]
rs7599863	1.00[ASN][1000 genomes]
rs7607203	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs883027	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9678669	0.81[GIH][hapmap];0.86[MEX][hapmap]
rs985919	1.00[JPT][hapmap]
rs9917332	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388948	chr2:50092667-50602681	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3399511	chr2:50092687-50602651	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv932915	chr2:50306630-50628415	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv492164	chr2:50399251-51029090	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1000653	chr2:50417660-51083470	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv535693	chr2:50417660-51083470	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1000087	chr2:50501395-50581229	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv948548	chr2:50569117-50695100	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6728741	ARHGAP26	cis	Frontal Cortex	GTEx
rs6728741	FBXO11	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50570600-50575400	Active TSS	Brain Angular Gyrus	brain
2	chr2:50572800-50575400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:50572800-50575400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr2:50573000-50575400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:50573000-50575600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr2:50573200-50575400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr2:50573400-50575400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr2:50573400-50575600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr2:50573600-50575400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr2:50573600-50575400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:50573800-50576000	Active TSS	Fetal Brain Female	brain
12	chr2:50574000-50575600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr2:50574400-50575400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:50575000-50575400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:50575000-50575400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
16	chr2:50575000-50575400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
17	chr2:50575000-50575400	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
18	chr2:50575000-50575400	Flanking Active TSS	Fetal Brain Male	brain
19	chr2:50575000-50575600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:50575200-50575400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
21	chr2:50575200-50575400	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr2:50575200-50575400	Bivalent Enhancer	Brain Hippocampus Middle	brain
23	chr2:50575200-50575400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
24	chr2:50575200-50575400	Bivalent Enhancer	Fetal Heart	heart
25	chr2:50575200-50575400	Bivalent Enhancer	Fetal Kidney	kidney
26	chr2:50575200-50575400	Bivalent Enhancer	Fetal Stomach	stomach
27	chr2:50575200-50575600	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr2:50575200-50575800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:50575200-50575800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links