Variant report

Variant	rs12751235
Chromosome Location	chr1:239869821-239869822
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	POLR2A	chr1:239869817-239870182	A549	lung:	n/a	n/a

Variant related genes	Relation type
CHRM3-AS2	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1014670	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1019881	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1019882	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10737838	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802793	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802794	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10802795	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10802798	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802801	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10802802	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10925964	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10925970	0.88[EUR][1000 genomes]
rs1134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1155611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11579382	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11583349	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11585281	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12029701	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12060884	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12118652	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12403497	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12403980	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12407154	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743042	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1416789	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1431719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1431721	0.91[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1544170	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2217532	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278642	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278644	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355237	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2355238	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429153	0.84[AMR][1000 genomes]
rs6429154	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663632	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6684622	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6695600	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7511970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7513746	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7513757	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7537514	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7552453	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs934344	0.86[EUR][1000 genomes];0.80[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	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv3377526	chr1:239623743-240111639	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv873351	chr1:239636613-240324200	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2757778	chr1:239766094-240389504	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv2759009	chr1:239766094-240389504	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239845000-239879800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:239861200-239878000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:239861400-239871600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:239866800-239875000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:239867400-239879000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr1:239867600-239875800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:239867800-239879000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:239868000-239870200	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:239868000-239871200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:239868000-239871400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:239868000-239871800	Strong transcription	Dnd41	blood
12	chr1:239868200-239870000	Weak transcription	Primary T cells from cord blood	blood
13	chr1:239868200-239870200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:239868400-239870800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr1:239868400-239871400	Weak transcription	Thymus	Thymus
16	chr1:239868400-239872200	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:239868600-239878200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:239868800-239880400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:239869000-239875800	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:239869000-239876000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:239869000-239880800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:239869600-239870200	Genic enhancers	Pancreas	Pancrea
23	chr1:239869800-239870000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:239869800-239870000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr1:239869800-239870200	Enhancers	H1 Cell Line	embryonic stem cell
26	chr1:239869800-239870200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:239869800-239870200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:239869800-239870200	Enhancers	H9 Cell Line	embryonic stem cell
29	chr1:239869800-239870200	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr1:239869800-239870200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:239869800-239870200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:239869800-239870200	Enhancers	Fetal Brain Male	brain
33	chr1:239869800-239870200	Genic enhancers	Gastric	stomach

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