Variant report

Variant	rs7944372
Chromosome Location	chr11:67897483-67897484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:67887526..67889554-chr11:67897461..67899656,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCIRG1-2	chr11:67896908-67897549	XLOC_009183
2	lnc-TCIRG1-2	chr11:67897265-67897549	ENSG00000255236.1
3	lnc-TCIRG1-2	chr11:67897317-67897549	NONHSAT022507

Variant related genes	Relation type
ENSG00000110721	Chromatin interaction
ENSG00000255236	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10791956	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10791957	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs10791959	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10896293	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10896295	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896298	0.80[JPT][hapmap];0.81[MEX][hapmap]
rs11228131	0.81[CHB][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes]
rs11228133	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11228136	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11228137	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11228139	1.00[CEU][hapmap]
rs11228141	0.84[ASN][1000 genomes]
rs11228142	1.00[CEU][hapmap]
rs11228144	0.94[JPT][hapmap]
rs11228145	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11535788	1.00[CEU][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1894204	0.80[JPT][hapmap];0.80[MEX][hapmap]
rs2075609	0.84[LWK][hapmap];0.82[MKK][hapmap]
rs2457179	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2457180	0.82[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs2511437	0.81[CHB][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs2511467	1.00[JPT][hapmap]
rs2511468	0.83[ASN][1000 genomes]
rs2511469	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2511470	0.82[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs2511472	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2511473	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2511475	0.82[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2511479	1.00[JPT][hapmap]
rs2512608	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2512611	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2512612	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2512623	0.92[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2512624	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3133327	0.88[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs3935460	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4073551	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4147780	0.82[CEU][hapmap];0.89[GIH][hapmap]
rs4345973	0.80[MEX][hapmap]
rs4420277	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4930557	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4930561	0.80[JPT][hapmap];0.81[MEX][hapmap]
rs61890478	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6591331	0.81[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6591333	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7104982	0.90[EUR][1000 genomes]
rs7123183	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7123668	0.91[EUR][1000 genomes]
rs7124058	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71480230	0.86[EUR][1000 genomes]
rs7925022	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7925423	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7928739	0.96[CEU][hapmap];0.87[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs7931502	0.80[JPT][hapmap];0.81[MEX][hapmap]
rs7940113	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940217	0.91[EUR][1000 genomes]
rs7940501	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884826	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427892	chr11:67451649-67926562	Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	nsv825963	chr11:67763676-68197054	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7944372	FGF19	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67889800-67897600	Enhancers	H1 Cell Line	embryonic stem cell
2	chr11:67892000-67897800	Enhancers	Pancreas	Pancrea
3	chr11:67894000-67898000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:67896200-67897800	Enhancers	H9 Cell Line	embryonic stem cell
5	chr11:67896600-67897600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:67896600-67897800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr11:67896600-67897800	Enhancers	Fetal Intestine Large	intestine
8	chr11:67896600-67897800	Enhancers	Fetal Intestine Small	intestine
9	chr11:67896800-67897600	Enhancers	HepG2	liver
10	chr11:67896800-67897800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr11:67896800-67900800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:67897000-67897800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
13	chr11:67897000-67905000	Weak transcription	Liver	Liver
14	chr11:67897200-67897600	Weak transcription	Esophagus	oesophagus
15	chr11:67897200-67898600	Weak transcription	Hela-S3	cervix
16	chr11:67897200-67907800	Weak transcription	Fetal Heart	heart
17	chr11:67897200-67908200	Weak transcription	Gastric	stomach
18	chr11:67897400-67898600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:67897400-67899400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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