Variant report

Variant	rs7773297
Chromosome Location	chr6:45961770-45961771
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1338470	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1338471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1361216	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1416170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1535108	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2022419	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2894658	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777612	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4714900	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458479	0.83[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap];0.98[MKK][hapmap];0.93[YRI][hapmap];0.86[ASN][1000 genomes]
rs6458480	1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap];0.86[ASN][1000 genomes]
rs6458481	0.86[ASN][1000 genomes]
rs6458482	0.86[ASN][1000 genomes]
rs6458483	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6921959	0.86[ASN][1000 genomes]
rs7772905	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];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9395142	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9472651	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9472653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9689698	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv428482	chr6:45926644-46050182	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv885867	chr6:45936223-45982976	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1025846	chr6:45955173-46047269	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7773297	TNFRSF21	cis	parietal	SCAN
rs7773297	POLR1C	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45953400-45965600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:45955800-45962200	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr6:45956800-45969000	Weak transcription	Fetal Intestine Small	intestine
4	chr6:45957000-45966000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:45957000-45969000	Weak transcription	Spleen	Spleen
6	chr6:45957000-45977400	Weak transcription	Fetal Intestine Large	intestine
7	chr6:45960400-45965600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:45960400-45970400	Weak transcription	Small Intestine	intestine
9	chr6:45960800-45961800	Weak transcription	Left Ventricle	heart
10	chr6:45960800-45965600	Weak transcription	Psoas Muscle	Psoas
11	chr6:45960800-45965600	Weak transcription	Right Ventricle	heart
12	chr6:45961400-45965200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:45961400-45965400	Weak transcription	Fetal Heart	heart

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