Variant report

Variant	rs6701938
Chromosome Location	chr1:48234949-48234950
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	POLR2A	chr1:48234916-48235864	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:48232346..48235008-chr1:48237593..48240015,2	K562	blood:

Variant related genes	Relation type
ENSG00000223814	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12037415	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12039958	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12406511	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2282361	0.81[EUR][1000 genomes]
rs3844086	0.81[TSI][hapmap]
rs3844087	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3850881	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs57078537	0.88[EUR][1000 genomes]
rs6693956	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs6698565	0.82[EUR][1000 genomes]
rs7520681	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829760	chr1:48111126-48308188	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv871257	chr1:48111699-48334490	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv871175	chr1:48150309-48254782	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1001126	chr1:48164622-48320862	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1003161	chr1:48207715-48286563	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv998583	chr1:48232131-48316877	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6701938	DMAP1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:48215400-48236200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:48218600-48239800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:48225600-48237000	Weak transcription	Fetal Intestine Large	intestine
4	chr1:48228000-48238800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:48228200-48238000	Weak transcription	Spleen	Spleen
6	chr1:48230400-48240000	Weak transcription	Aorta	Aorta
7	chr1:48230400-48246600	Weak transcription	Esophagus	oesophagus
8	chr1:48231200-48237400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:48231200-48247000	Weak transcription	Gastric	stomach
10	chr1:48231400-48235200	Enhancers	Left Ventricle	heart
11	chr1:48231400-48236200	Enhancers	Fetal Heart	heart
12	chr1:48231600-48237000	Weak transcription	Fetal Intestine Small	intestine
13	chr1:48232000-48235400	Enhancers	Right Ventricle	heart
14	chr1:48232000-48238600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:48232200-48237400	Enhancers	Fetal Muscle Leg	muscle
16	chr1:48233600-48235200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:48234000-48235200	Weak transcription	Right Atrium	heart
18	chr1:48234000-48236400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr1:48234000-48237000	Weak transcription	Pancreas	Pancrea
20	chr1:48234000-48240400	Weak transcription	Liver	Liver
21	chr1:48234400-48235600	Enhancers	Fetal Lung	lung
22	chr1:48234600-48235000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:48234600-48235400	Enhancers	Brain Germinal Matrix	brain
24	chr1:48234600-48235600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
25	chr1:48234600-48235600	Enhancers	Fetal Stomach	stomach
26	chr1:48234600-48236200	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links