Variant report

Variant	rs12155449
Chromosome Location	chr7:139475320-139475321
allele	C/T
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	SMC3	chr7:139473945-139477093	SK-N-SH	brain:	n/a	n/a
2	RAD21	chr7:139475152-139477208	SK-N-SH	brain:	n/a	chr7:139475362-139475371
3	CTCF	chr7:139475180-139475330	HMF	breast:	n/a	n/a
4	RAD21	chr7:139475296-139476990	IMR90	lung:	n/a	chr7:139475362-139475371
5	POLR2A	chr7:139474972-139478525	MCF10A-Er-Src	breast:	n/a	n/a
6	MXI1	chr7:139474826-139479222	SK-N-SH	brain:	n/a	n/a
7	MXI1	chr7:139473683-139479282	IMR90	lung:	n/a	n/a
8	CTCF	chr7:139475215-139476209	A549	lung:	n/a	chr7:139475859-139475872 chr7:139475771-139475789 chr7:139475499-139475507
9	CTCF	chr7:139473870-139477037	SK-N-SH	brain:	n/a	chr7:139475859-139475872 chr7:139474878-139474899 chr7:139475771-139475789 chr7:139475499-139475507
10	CTCF	chr7:139475300-139475450	AG09309	skin:	n/a	n/a
11	CTCF	chr7:139475240-139475390	HRPEpiC	eye:	n/a	n/a
12	CTCF	chr7:139475220-139475370	HCPEpiC	choroid plexus:	n/a	n/a
13	POLR2A	chr7:139474250-139477073	MCF10A-Er-Src	breast:	n/a	n/a
14	SMC3	chr7:139475313-139475352	GM12878	blood:	n/a	n/a
15	CTCF	chr7:139475200-139475350	GM12872	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:139474504..139476170-chr7:139702174..139703721,2	K562	blood:
2	chr7:139473245..139475405-chr7:139553701..139555890,2	K562	blood:
3	chr7:139475307..139476323-chr7:139701274..139702359,4	MCF-7	breast:
4	chr7:139466166..139468375-chr7:139473040..139475518,2	MCF-7	breast:
5	chr7:139328556..139330958-chr7:139473261..139475609,2	K562	blood:
6	chr7:139474297..139476701-chr7:139704235..139706049,2	K562	blood:

Variant related genes	Relation type
TBXAS1	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1015121	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224408	0.83[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs10230692	0.88[EUR][1000 genomes]
rs10254826	0.90[EUR][1000 genomes]
rs10268753	0.88[EUR][1000 genomes]
rs10278124	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs1106768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374779	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12374780	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177103	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177358	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177953	0.81[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17262390	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17262662	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17262676	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074826	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs4074827	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs55826011	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56079671	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56840127	0.86[EUR][1000 genomes]
rs61054086	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967634	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73158611	0.90[EUR][1000 genomes]
rs73158613	0.90[EUR][1000 genomes]
rs73158614	0.90[EUR][1000 genomes]
rs73158616	0.89[EUR][1000 genomes]
rs73735624	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs740818	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787807	0.90[EUR][1000 genomes]
rs7793114	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7798740	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12155449	LOC730441	cis	parietal	SCAN
rs12155449	TBXAS1	cis	parietal	SCAN
rs12155449	RAB19	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:139446600-139475800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr7:139446600-139476400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:139446800-139476400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:139467600-139475400	Weak transcription	Aorta	Aorta
5	chr7:139468000-139475800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:139468800-139475600	Enhancers	Primary T cells from cord blood	blood
7	chr7:139469000-139475400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:139469000-139475600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr7:139469200-139475400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr7:139469200-139475800	Weak transcription	Esophagus	oesophagus
11	chr7:139469200-139476200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:139469200-139476400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:139469800-139475800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:139470400-139475400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr7:139470600-139475600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr7:139471400-139475800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:139471600-139475800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr7:139471800-139475400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr7:139472000-139475400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr7:139472000-139475400	Weak transcription	Small Intestine	intestine
21	chr7:139472000-139475600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr7:139472000-139475600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr7:139472600-139475400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr7:139472600-139475800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr7:139472800-139475400	Enhancers	NHDF-Ad	bronchial
26	chr7:139472800-139475800	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr7:139472800-139475800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
28	chr7:139472800-139475800	Flanking Active TSS	GM12878-XiMat	blood
29	chr7:139473000-139475600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr7:139473000-139475600	Enhancers	Placenta Amnion	Placenta Amnion
31	chr7:139473600-139475400	Enhancers	Hela-S3	cervix
32	chr7:139473600-139475400	Enhancers	HSMMtube	muscle
33	chr7:139473800-139475400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:139474000-139475400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr7:139474000-139475400	Enhancers	HUVEC	blood vessel
36	chr7:139474000-139475800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr7:139474000-139475800	Enhancers	Fetal Heart	heart
38	chr7:139474200-139475600	Weak transcription	Gastric	stomach
39	chr7:139474200-139475600	Enhancers	K562	blood
40	chr7:139474200-139475800	Flanking Active TSS	A549	lung
41	chr7:139474400-139475400	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr7:139474400-139475400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr7:139474400-139475600	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr7:139474400-139475800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr7:139474400-139475800	Enhancers	Fetal Intestine Large	intestine
46	chr7:139474400-139476200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr7:139474600-139475400	Enhancers	Stomach Smooth Muscle	stomach
48	chr7:139474600-139475600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr7:139474600-139475600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr7:139474600-139475800	Flanking Active TSS	Adipose Nuclei	Adipose

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