Variant report

Variant	rs274622
Chromosome Location	chr7:86272940-86272941
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	E2F6	chr7:86272884-86274944	H1-hESC	embryonic stem cell:	n/a	chr7:86274844-86274856
2	GATA2	chr7:86272858-86274979	SH-SY5Y	brain:	n/a	chr7:86274815-86274827 chr7:86273773-86273789 chr7:86274817-86274824 chr7:86273138-86273154 chr7:86274817-86274824 chr7:86274816-86274826 chr7:86273767-86273784 chr7:86274817-86274824 chr7:86273770-86273778 chr7:86273138-86273154 chr7:86274813-86274829
3	TAF1	chr7:86272850-86273421	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr7:86272783-86273528	H1-neurons	neurons:	n/a	n/a
5	REST	chr7:86272554-86274254	H1-neurons	neurons:	n/a	chr7:86273954-86273967
6	POLR2A	chr7:86272716-86273508	H1-neurons	neurons:	n/a	n/a
7	GATA3	chr7:86272600-86272980	T-47D	breast:	n/a	chr7:86272769-86272786

Variant related genes	Relation type
GRM3	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10241183	0.88[EUR][1000 genomes]
rs12333697	0.88[ASN][1000 genomes]
rs166677	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs200839	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2107691	0.87[ASN][1000 genomes]
rs2204638	0.88[EUR][1000 genomes]
rs2299212	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2463398	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2526952	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs274613	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs274614	0.88[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs274616	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs274617	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs274618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs274619	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs274620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs274621	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs274623	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs274624	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs274625	0.83[ASN][1000 genomes]
rs274628	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs274629	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs274630	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs274631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs274633	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs274634	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs274636	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs274637	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62488405	0.88[EUR][1000 genomes]
rs701334	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs701335	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs701336	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs701337	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs701338	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs724225	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs724226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7794681	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs802420	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs802421	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs802423	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs802426	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs802427	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs802428	0.81[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs802430	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs802431	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs802433	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs802434	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs802435	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs802436	0.81[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs802437	0.81[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs802438	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs802440	0.83[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs802442	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs802443	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs802445	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs802446	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs802447	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs802449	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs802450	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs802456	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs802459	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.92[ASN][1000 genomes]
rs802465	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs802466	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs802475	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]

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	nsv1025032	chr7:86032479-86642973	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv831053	chr7:86268171-86440999	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs274622	DMTF1	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86272600-86273000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr7:86272600-86273000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr7:86272600-86273200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:86272600-86273200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:86272600-86273400	Active TSS	H1 Cell Line	embryonic stem cell
6	chr7:86272600-86273400	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr7:86272600-86273600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:86272600-86274000	Active TSS	Fetal Brain Female	brain
9	chr7:86272600-86274600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:86272600-86275000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr7:86272600-86275200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr7:86272600-86275400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:86272600-86275600	Active TSS	Fetal Brain Male	brain
14	chr7:86272600-86277200	Active TSS	Brain Hippocampus Middle	brain
15	chr7:86272600-86277200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:86272600-86277400	Active TSS	Brain Angular Gyrus	brain
17	chr7:86272600-86277800	Active TSS	Brain Cingulate Gyrus	brain
18	chr7:86272600-86278000	Active TSS	Brain Anterior Caudate	brain
19	chr7:86272600-86278000	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr7:86272800-86273000	Bivalent Enhancer	Fetal Stomach	stomach
21	chr7:86272800-86273000	Enhancers	Right Ventricle	heart
22	chr7:86272800-86273000	Bivalent Enhancer	NH-A	brain
23	chr7:86272800-86273200	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr7:86272800-86273200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
25	chr7:86272800-86273400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:86272800-86273400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr7:86272800-86273600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr7:86272800-86273600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr7:86272800-86274200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:86272800-86274200	Active TSS	Right Atrium	heart
31	chr7:86272800-86274600	Active TSS	H9 Cell Line	embryonic stem cell
32	chr7:86272800-86274600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
33	chr7:86272800-86274600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr7:86272800-86274600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
35	chr7:86272800-86274800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
36	chr7:86272800-86274800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr7:86272800-86274800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
38	chr7:86272800-86274800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
39	chr7:86272800-86275000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:86272800-86275800	Active TSS	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links