Variant report

Variant	rs7511970
Chromosome Location	chr1:239883255-239883256
allele	A/G
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	REST	chr1:239882829-239883516	HL-60	blood:	n/a	n/a
2	POLR2A	chr1:239882822-239883468	HL-60	blood:	n/a	n/a
3	MYC	chr1:239881907-239883553	NB4	blood:	n/a	chr1:239883185-239883195
4	POLR2A	chr1:239882270-239883651	NB4	blood:	n/a	n/a
5	MAX	chr1:239881010-239883868	NB4	blood:	n/a	chr1:239883185-239883195
6	POLR2A	chr1:239882863-239883417	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
CHRM3-AS2	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1014670	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1019881	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1019882	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10737838	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10802793	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10802794	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10802795	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10802798	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10802801	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10802802	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10925964	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10925970	0.89[EUR][1000 genomes]
rs1134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1155611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11579382	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11583349	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11585281	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12029701	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12060884	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12118652	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12403497	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12403980	0.82[AFR][1000 genomes]
rs12407154	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12743042	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12751235	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]
rs1416789	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1431719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431721	0.88[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1544170	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2217532	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278642	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278643	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278644	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2355237	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2355238	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6429153	0.81[AMR][1000 genomes]
rs6429154	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6663632	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6684622	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6695600	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs717227	0.85[GIH][hapmap]
rs7513746	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7513757	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7537514	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7552453	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs891700	0.85[GIH][hapmap]
rs934344	0.85[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7511970	RBM34	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239875400-239890800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:239878200-239891000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:239880000-239885800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:239880400-239884000	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr1:239880400-239885600	Active TSS	Primary T cells fromperipheralblood	blood
6	chr1:239880600-239884600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:239880800-239883800	Active TSS	Duodenum Mucosa	Duodenum
8	chr1:239881000-239884200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:239881000-239884400	Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr1:239881000-239885400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr1:239881200-239884200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:239881200-239884400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
13	chr1:239881400-239884800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:239881800-239883400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr1:239881800-239884600	Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr1:239882200-239883600	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr1:239882200-239884000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr1:239882200-239884200	Active TSS	Primary B cells from cord blood	blood
19	chr1:239882400-239883400	Enhancers	Pancreas	Pancrea
20	chr1:239882400-239883600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr1:239882400-239885000	Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr1:239882600-239884000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:239882800-239883400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr1:239882800-239883400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr1:239882800-239883400	Enhancers	Brain Angular Gyrus	brain
26	chr1:239882800-239883400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr1:239882800-239883400	Bivalent Enhancer	Stomach Mucosa	stomach
28	chr1:239882800-239883800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:239882800-239883800	Active TSS	Right Atrium	heart
30	chr1:239882800-239884200	Active TSS	Primary T cells from cord blood	blood
31	chr1:239883000-239883400	Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr1:239883000-239883400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:239883000-239883400	Active TSS	Colonic Mucosa	Colon
34	chr1:239883000-239883400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr1:239883000-239883400	Active TSS	Fetal Brain Male	brain
36	chr1:239883000-239883400	Active TSS	Gastric	stomach
37	chr1:239883000-239883400	Active TSS	Rectal Smooth Muscle	rectum
38	chr1:239883000-239884200	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr1:239883000-239884200	Active TSS	Dnd41	blood
40	chr1:239883000-239884400	Active TSS	Thymus	Thymus
41	chr1:239883200-239883400	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr1:239883200-239883400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr1:239883200-239883400	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr1:239883200-239883400	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr1:239883200-239883800	Active TSS	Primary B cells from peripheral blood	blood
46	chr1:239883200-239883800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:239883200-239884800	Active TSS	Fetal Thymus	thymus

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