Variant report

Variant	rs6966824
Chromosome Location	chr7:15198589-15198590
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10950555	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10950556	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10950557	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12666714	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12667178	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12667930	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12699689	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12699690	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13233339	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13438104	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2191992	0.81[ASN][1000 genomes]
rs2191993	0.84[ASN][1000 genomes]
rs2215652	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2389406	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2389407	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2389408	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2908327	0.96[ASN][1000 genomes]
rs2908328	0.86[ASN][1000 genomes]
rs2908333	0.95[ASN][1000 genomes]
rs2961235	0.83[ASN][1000 genomes]
rs2961236	0.80[ASN][1000 genomes]
rs2961268	0.84[ASN][1000 genomes]
rs35170332	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35557899	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4565367	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57525864	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][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	esv2758104	chr7:14896877-15299786	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv2759512	chr7:14896877-15299786	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1032569	chr7:14905287-15597069	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1021172	chr7:14944318-15548794	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv538743	chr7:14944318-15548794	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv517876	chr7:15010824-15198589	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv830910	chr7:15011028-15212309	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv522976	chr7:15108184-15318473	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv606292	chr7:15121951-15262599	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1029203	chr7:15138771-15267341	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv538744	chr7:15138771-15267341	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1017877	chr7:15171708-15395476	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv433033	chr7:15172260-15226660	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv1017559	chr7:15173335-15374132	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv538745	chr7:15173335-15374132	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv1024435	chr7:15174484-15309359	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6966824	AGR2	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:15195400-15200600	Enhancers	Colon Smooth Muscle	Colon
2	chr7:15196000-15199200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr7:15197000-15198800	Enhancers	Rectal Smooth Muscle	rectum
4	chr7:15197800-15199200	Enhancers	Fetal Muscle Leg	muscle
5	chr7:15197800-15199400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:15197800-15199600	Enhancers	Ovary	ovary
7	chr7:15197800-15199800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr7:15197800-15199800	Enhancers	Fetal Stomach	stomach
9	chr7:15197800-15200000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:15198200-15198600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr7:15198200-15199800	Enhancers	Stomach Smooth Muscle	stomach
12	chr7:15198400-15199200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links