Variant report

Variant	rs1019178
Chromosome Location	chr7:139525624-139525625
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr7:139525412-139526289	K562	blood:	n/a	chr7:139525906-139525918 chr7:139525907-139525917 chr7:139525907-139525916 chr7:139525904-139525915 chr7:139525908-139525917
2	JUND	chr7:139525214-139526579	SK-N-SH	brain:	n/a	chr7:139525906-139525917 chr7:139525906-139525918 chr7:139525907-139525917 chr7:139525907-139525916 chr7:139525904-139525915 chr7:139525908-139525917
3	TCF12	chr7:139525315-139526259	SK-N-SH	brain:	n/a	chr7:139525316-139525326
4	FOSL2	chr7:139525576-139526179	SK-N-SH	brain:	n/a	chr7:139525906-139525918 chr7:139525907-139525917 chr7:139525907-139525916 chr7:139525904-139525915 chr7:139525908-139525917

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:139517568..139521373-chr7:139521587..139526613,5	K562	blood:
2	chr7:139524710..139527393-chr7:139527540..139530071,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLEC2L-2	chr7:139523530-139525908	l_3489_NR_024451

Variant related genes	Relation type
TBXAS1	TF binding region
ENSG00000059377	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10228337	0.92[EUR][1000 genomes]
rs10233386	0.92[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs10253277	0.81[GIH][hapmap]
rs10256282	0.80[GIH][hapmap]
rs10277434	0.92[EUR][1000 genomes]
rs10277664	0.82[GIH][hapmap]
rs10277705	0.81[JPT][hapmap]
rs1107952	0.85[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs12532701	0.89[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs12534299	0.81[GIH][hapmap]
rs2267679	0.81[GIH][hapmap]
rs2267680	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2267681	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4590360	0.81[GIH][hapmap]
rs4726997	0.87[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56168252	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60503820	0.92[EUR][1000 genomes]
rs6953224	0.82[YRI][hapmap]
rs6960593	0.92[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs6969517	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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6972693	0.80[ASN][1000 genomes]
rs723670	0.96[EUR][1000 genomes]
rs764746	0.81[GIH][hapmap]
rs7804587	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8192803	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020234	chr7:139377822-139661964	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1032711	chr7:139411404-139684043	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv464732	chr7:139424022-139654256	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv608472	chr7:139424022-139654256	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1018712	chr7:139429703-139658014	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv464733	chr7:139491967-139539218	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv608473	chr7:139491967-139539218	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1019178	RAB19	cis	parietal	SCAN
rs1019178	TAS2R5	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:139517200-139529200	Weak transcription	Right Atrium	heart
2	chr7:139519200-139528200	Weak transcription	Gastric	stomach
3	chr7:139523200-139526400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr7:139523400-139526200	Enhancers	Fetal Stomach	stomach
5	chr7:139523400-139526400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr7:139523800-139526200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:139524200-139525800	Enhancers	Fetal Kidney	kidney
8	chr7:139524600-139526400	Enhancers	Fetal Lung	lung
9	chr7:139524800-139526200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:139525000-139526200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:139525000-139526200	Enhancers	NHLF	lung
12	chr7:139525200-139526000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr7:139525200-139526200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr7:139525200-139526200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr7:139525200-139526200	Enhancers	Osteobl	bone
16	chr7:139525400-139525800	Enhancers	HSMMtube	muscle
17	chr7:139525400-139526000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:139525400-139526000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr7:139525400-139526200	Enhancers	NH-A	brain
20	chr7:139525400-139526200	Enhancers	NHDF-Ad	bronchial
21	chr7:139525400-139526400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr7:139525400-139528400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr7:139525600-139526200	Enhancers	HSMM	muscle
24	chr7:139525600-139526200	Bivalent Enhancer	K562	blood
25	chr7:139525600-139526400	Enhancers	HMEC	breast
26	chr7:139525600-139528200	Weak transcription	Placenta	Placenta
27	chr7:139525600-139529000	Weak transcription	Ovary	ovary

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