Variant report

Variant	rs4073643
Chromosome Location	chr7:104486707-104486708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10085831	0.94[CEU][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10258340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28465113	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28526655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4073894	0.89[CEU][hapmap];0.91[GIH][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap]
rs4144809	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59449150	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71562617	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73184012	0.91[EUR][1000 genomes]

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	nsv429790	chr7:104314049-104488049	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv429792	chr7:104400049-104488049	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv5887	chr7:104401250-104491604	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv522743	chr7:104411273-104486707	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv831086	chr7:104422503-104596766	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4073643	RINT1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104466000-104486800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr7:104476400-104503000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr7:104479600-104488800	Weak transcription	Colon Smooth Muscle	Colon
4	chr7:104481600-104514400	Weak transcription	Fetal Kidney	kidney
5	chr7:104483600-104487200	Strong transcription	Fetal Intestine Large	intestine
6	chr7:104483600-104493000	Weak transcription	Pancreas	Pancrea
7	chr7:104486000-104489400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:104486200-104487800	Enhancers	Brain Substantia Nigra	brain
9	chr7:104486200-104489200	Enhancers	Brain Cingulate Gyrus	brain
10	chr7:104486200-104492800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:104486400-104486800	Enhancers	Brain Anterior Caudate	brain
12	chr7:104486400-104487000	Weak transcription	Brain Hippocampus Middle	brain
13	chr7:104486400-104487400	Weak transcription	Fetal Intestine Small	intestine
14	chr7:104486600-104487600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr7:104486600-104492600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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