Variant report

Variant	rs12141357
Chromosome Location	chr1:171226217-171226218
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	NFIC	chr1:171226170-171226894	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr1:171226195-171226342	SH-SY5Y	brain:	n/a	n/a
3	MXI1	chr1:171226109-171226748	SK-N-SH	brain:	n/a	n/a
4	MYC	chr1:171226132-171226644	MCF10A-Er-Src	breast:	n/a	chr1:171226442-171226452 chr1:171226496-171226505 chr1:171226496-171226506
5	CEBPB	chr1:171226110-171226695	MCF-7	breast:	n/a	chr1:171226386-171226397
6	MYC	chr1:171226101-171226673	MCF10A-Er-Src	breast:	n/a	chr1:171226442-171226452 chr1:171226496-171226505 chr1:171226496-171226506
7	STAT3	chr1:171226171-171226549	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr1:171226157-171226560	MCF10A-Er-Src	breast:	n/a	n/a
9	GATA2	chr1:171226094-171226957	SH-SY5Y	brain:	n/a	n/a
10	CEBPB	chr1:171226215-171226600	Hela-S3	cervix:	n/a	chr1:171226386-171226397
11	E2F4	chr1:171226101-171226561	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
FMO1	TF binding region
ENSG00000206692	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12065835	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs12139312	0.83[EUR][1000 genomes]
rs12142448	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs12142492	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12144402	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12145368	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28360369	1.00[EUR][1000 genomes]
rs28384856	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28384863	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs36104491	1.00[AFR][1000 genomes]
rs6674736	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs6699345	1.00[CEU][hapmap];0.85[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171221000-171226600	Weak transcription	Esophagus	oesophagus
2	chr1:171221000-171227600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:171221200-171226400	Weak transcription	Right Atrium	heart
4	chr1:171221200-171227200	Enhancers	Fetal Intestine Small	intestine
5	chr1:171221200-171228200	Enhancers	Fetal Intestine Large	intestine
6	chr1:171221800-171226400	Weak transcription	Pancreas	Pancrea
7	chr1:171221800-171226800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:171221800-171226800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:171222000-171226400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:171222000-171226600	Weak transcription	Placenta	Placenta
11	chr1:171222000-171227200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:171222000-171227400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:171224400-171227200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:171224600-171226400	Weak transcription	Gastric	stomach
15	chr1:171224800-171226600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:171224800-171227400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:171224800-171227800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:171225000-171226400	Weak transcription	Small Intestine	intestine
19	chr1:171225000-171226400	Weak transcription	NHDF-Ad	bronchial
20	chr1:171225000-171227200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:171225000-171227600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:171225000-171228000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:171225600-171227200	Enhancers	Fetal Muscle Leg	muscle
24	chr1:171226000-171226800	Enhancers	Liver	Liver
25	chr1:171226000-171226800	Enhancers	Fetal Kidney	kidney
26	chr1:171226000-171226800	Enhancers	Fetal Lung	lung
27	chr1:171226000-171226800	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr1:171226000-171227200	Enhancers	HMEC	breast
29	chr1:171226000-171227400	Enhancers	Duodenum Mucosa	Duodenum
30	chr1:171226000-171228000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:171226000-171228600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:171226000-171228800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:171226000-171228800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:171226000-171228800	Enhancers	NHEK	skin
35	chr1:171226000-171229200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:171226200-171226600	Enhancers	Fetal Muscle Trunk	muscle
37	chr1:171226200-171226800	Enhancers	Colonic Mucosa	Colon
38	chr1:171226200-171227000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:171226200-171227000	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr1:171226200-171227000	Enhancers	Stomach Mucosa	stomach
41	chr1:171226200-171227800	Enhancers	Fetal Heart	heart
42	chr1:171226200-171228800	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr1:171226200-171229200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links