Variant report

Variant	rs670671
Chromosome Location	chr18:12862942-12862943
allele	G/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	FOS	chr18:12862509-12863032	MCF10A-Er-Src	breast:	n/a	n/a
2	TEAD4	chr18:12862494-12862968	H1-hESC	embryonic stem cell:	n/a	n/a
3	STAT3	chr18:12862641-12863075	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr18:12862371-12862951	H1-hESC	embryonic stem cell:	n/a	n/a
5	STAT3	chr18:12862517-12862950	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr18:12862757-12862947	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr18:12862494-12863029	MCF10A-Er-Src	breast:	n/a	n/a
8	JUND	chr18:12862450-12863023	H1-hESC	embryonic stem cell:	n/a	chr18:12862467-12862479
9	MAZ	chr18:12862868-12863026	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12862494..12865307-chr18:12880258..12883236,3	MCF-7	breast:

Variant related genes	Relation type
PTPN2	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs2292758	0.83[ASN][1000 genomes]
rs2847288	0.80[ASN][1000 genomes]
rs3826556	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45579734	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs471401	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4797707	0.96[ASN][1000 genomes]
rs4797708	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs502763	0.89[EUR][1000 genomes]
rs507304	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578377	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs579052	0.95[AFR][1000 genomes]
rs58200120	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59471125	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs607906	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622717	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs637643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505769	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs669822	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683468	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7238238	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7241650	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73950681	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73950683	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73950684	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73950685	0.84[ASN][1000 genomes]
rs8084365	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8091305	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8098730	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9954778	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9959061	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9959425	0.90[AFR][1000 genomes]
rs9961827	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9961931	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9966378	0.88[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	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
4	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12838800-12879000	Weak transcription	Psoas Muscle	Psoas
2	chr18:12840000-12863800	Weak transcription	Brain Anterior Caudate	brain
3	chr18:12841000-12863200	Weak transcription	Colonic Mucosa	Colon
4	chr18:12841400-12863400	Weak transcription	Esophagus	oesophagus
5	chr18:12844200-12879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr18:12852000-12863200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr18:12852400-12863000	Weak transcription	NHLF	lung
8	chr18:12854800-12864000	Weak transcription	Brain Substantia Nigra	brain
9	chr18:12856600-12863000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr18:12856600-12863400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr18:12856600-12863600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr18:12856600-12863600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr18:12857000-12863200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr18:12857400-12863000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr18:12857400-12863600	Weak transcription	Aorta	Aorta
16	chr18:12857400-12863800	Enhancers	Fetal Thymus	thymus
17	chr18:12857400-12872000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr18:12857800-12863000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr18:12857800-12866200	Weak transcription	HSMMtube	muscle
20	chr18:12857800-12867600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr18:12857800-12881600	Weak transcription	Fetal Stomach	stomach
22	chr18:12858000-12872600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr18:12858600-12867400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr18:12859600-12867000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr18:12859600-12876800	Weak transcription	Primary T cells from cord blood	blood
26	chr18:12859800-12866600	Enhancers	Dnd41	blood
27	chr18:12860400-12863800	Enhancers	Primary B cells from peripheral blood	blood
28	chr18:12861000-12864000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr18:12861000-12864400	Enhancers	Primary B cells from cord blood	blood
30	chr18:12861200-12863200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr18:12861200-12863400	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr18:12861200-12863400	Enhancers	HMEC	breast
33	chr18:12861200-12863600	Enhancers	Fetal Intestine Large	intestine
34	chr18:12861200-12863800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr18:12861400-12863200	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr18:12861400-12863600	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr18:12861400-12865200	Enhancers	Fetal Lung	lung
38	chr18:12861600-12863000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr18:12861600-12863400	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr18:12861600-12863400	Enhancers	Fetal Muscle Leg	muscle
41	chr18:12861600-12863400	Enhancers	NHEK	skin
42	chr18:12861600-12863800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr18:12861600-12863800	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr18:12861600-12865000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr18:12861800-12870000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr18:12861800-12872600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr18:12862000-12863000	Enhancers	Primary hematopoietic stem cells	blood
48	chr18:12862000-12863200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr18:12862000-12863200	Weak transcription	Fetal Intestine Small	intestine
50	chr18:12862200-12863000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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