Variant report

Variant	rs10953453
Chromosome Location	chr7:104491613-104491614
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10226913	0.91[EUR][1000 genomes]
rs10226989	0.89[EUR][1000 genomes]
rs10252576	0.90[CEU][hapmap]
rs10267013	0.89[EUR][1000 genomes]
rs11762138	0.90[CHB][hapmap];0.90[YRI][hapmap]
rs12055895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12667640	0.81[CHB][hapmap]
rs12672828	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17706774	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005888	0.82[EUR][1000 genomes]
rs2192931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385466	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3955473	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4382394	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4532541	0.90[CHB][hapmap];0.90[YRI][hapmap]
rs4571661	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs4730052	0.93[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4730053	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59264482	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59335487	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59814386	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62485395	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62485396	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6466028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6958846	0.95[CEU][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs741323	0.90[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs9885984	0.87[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10953453	FAM185A	cis	cerebellum	SCAN
rs10953453	SLC26A4	cis	cerebellum	SCAN
rs10953453	LRWD1	cis	parietal	SCAN
rs10953453	RINT1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104476400-104503000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr7:104481600-104514400	Weak transcription	Fetal Kidney	kidney
3	chr7:104483600-104493000	Weak transcription	Pancreas	Pancrea
4	chr7:104486200-104492800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:104486600-104492600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:104489000-104492400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr7:104489000-104493400	Weak transcription	Fetal Intestine Large	intestine
8	chr7:104489000-104493800	Weak transcription	Fetal Brain Male	brain
9	chr7:104489000-104494400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:104489200-104492400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr7:104489400-104492200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr7:104490000-104492200	Weak transcription	Fetal Intestine Small	intestine
13	chr7:104490800-104491800	Enhancers	GM12878-XiMat	blood
14	chr7:104491000-104492400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr7:104491400-104493400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:104491400-104493400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:104491600-104493600	Enhancers	Adipose Nuclei	Adipose

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