Variant report

Variant	rs12091786
Chromosome Location	chr1:171768793-171768794
allele	A/C
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	chr1:171767253-171768989	Hela-S3	cervix:	n/a	n/a
2	GATA3	chr1:171768040-171768803	MCF-7	breast:	n/a	chr1:171768632-171768639 chr1:171768632-171768639 chr1:171768629-171768639 chr1:171768516-171768529 chr1:171768632-171768639
3	POLR2A	chr1:171766142-171769839	K562	blood:	n/a	n/a
4	POLR2A	chr1:171768599-171768858	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:171750108..171754190-chr1:171766349..171769659,4	K562	blood:
2	chr1:171768198..171768986-chr1:171952792..171953344,2	MCF-7	breast:
3	chr1:171768042..171770155-chr1:171772867..171774422,2	MCF-7	breast:
4	chr1:171709806..171712029-chr1:171768013..171770054,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213060	TF binding region
ENSG00000010165	Chromatin interaction
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1045456	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489252	0.94[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12565176	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs12567851	0.87[EUR][1000 genomes]
rs12730717	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12742601	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12750330	0.88[EUR][1000 genomes]
rs12753043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17596025	0.94[CEU][hapmap];0.99[EUR][1000 genomes]
rs17596081	0.94[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs17649609	0.94[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17650310	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17650340	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17657363	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1801898	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143369	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181216	0.94[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs2223602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2232807	0.84[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232813	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232819	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232824	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232825	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294718	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs236894	0.94[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs236897	0.86[EUR][1000 genomes]
rs236898	0.86[EUR][1000 genomes]
rs236899	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs236900	0.87[EUR][1000 genomes]
rs236907	0.94[CEU][hapmap]
rs34320898	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34627492	0.88[EUR][1000 genomes]
rs35249022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35400839	0.99[EUR][1000 genomes]
rs35631282	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35674909	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35882887	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35930163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36080557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3891278	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55732843	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56365362	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56377810	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61807979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656852	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674364	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs6675708	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs6681322	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6687624	0.90[JPT][hapmap]
rs6689125	0.94[EUR][1000 genomes]
rs6695933	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7522582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers 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 miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12091786	METTL13	cis	cerebellum	SCAN
rs12091786	VAMP4	cis	cerebellum	SCAN
rs12091786	RHOA	trans	parietal	SCAN
rs12091786	DUSP27	cis	parietal	SCAN
rs12091786	EFNB2	trans	lymphoblastoid	seeQTL
rs12091786	PIGC	cis	parietal	SCAN
rs12091786	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL
rs12091786	MAEL	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171751600-171770800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:171752000-171773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:171752800-171770200	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr1:171754200-171769600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:171754200-171770200	Strong transcription	Primary T cells from cord blood	blood
6	chr1:171754200-171770200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:171754800-171768800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:171763800-171770400	Weak transcription	Small Intestine	intestine
9	chr1:171765000-171774600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:171765600-171770800	Weak transcription	Hela-S3	cervix
11	chr1:171766000-171772800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:171766000-171774800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:171766200-171769000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:171766200-171774400	Weak transcription	Brain Substantia Nigra	brain
15	chr1:171766200-171774600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:171766200-171774600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:171766200-171775400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:171766200-171777200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:171766400-171770200	Weak transcription	NH-A	brain
20	chr1:171766400-171777200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:171766600-171770200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:171766600-171770800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:171766600-171774600	Weak transcription	Ovary	ovary
24	chr1:171766600-171774800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:171766600-171774800	Weak transcription	Placenta	Placenta
26	chr1:171766600-171774800	Weak transcription	HepG2	liver
27	chr1:171766800-171770400	Weak transcription	Brain Hippocampus Middle	brain
28	chr1:171766800-171770400	Weak transcription	Fetal Kidney	kidney
29	chr1:171766800-171771800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:171766800-171772800	Weak transcription	Right Ventricle	heart
31	chr1:171766800-171774600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:171766800-171774600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:171767000-171769000	Weak transcription	HSMMtube	muscle
34	chr1:171767000-171769200	Weak transcription	Colonic Mucosa	Colon
35	chr1:171767000-171770400	Weak transcription	Brain Angular Gyrus	brain
36	chr1:171767000-171770800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:171767000-171770800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:171767000-171771600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:171767000-171774600	Weak transcription	K562	blood
40	chr1:171767000-171774800	Weak transcription	Osteobl	bone
41	chr1:171767000-171777200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:171767000-171778600	Weak transcription	NHEK	skin
43	chr1:171767200-171770200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:171767200-171774600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:171767200-171774800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:171767200-171774800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:171767200-171777600	Weak transcription	HMEC	breast
48	chr1:171767400-171769200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:171767400-171769600	Weak transcription	Primary B cells from cord blood	blood
50	chr1:171767400-171770200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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