Variant report

Variant	rs1801898
Chromosome Location	chr1:171765964-171765965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171754075..171756411-chr1:171764040..171766145,2	MCF-7	breast:
2	chr1:171764717..171768373-chr1:171769892..171773572,7	K562	blood:
3	chr1:171755451..171759519-chr1:171762178..171766070,4	MCF-7	breast:
4	chr1:171749779..171754190-chr1:171762974..171767849,5	K562	blood:

Variant related genes	Relation type
ENSG00000010165	Chromatin interaction
ENSG00000213060	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1045456	1.00[ASW][hapmap];1.00[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	1.00[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]
rs12091786	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]
rs12565176	1.00[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	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs17596081	1.00[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs17649609	1.00[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17650310	0.92[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];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]
rs2143369	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181216	1.00[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs2223602	0.94[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];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	1.00[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];1.00[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	1.00[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs236894	1.00[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	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs236900	0.87[EUR][1000 genomes]
rs236907	1.00[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	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6675708	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6681322	0.84[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];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	0.94[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1801898	METTL13	cis	cerebellum	SCAN
rs1801898	VAMP4	cis	cerebellum	SCAN
rs1801898	RHOA	trans	parietal	SCAN
rs1801898	DUSP27	cis	parietal	SCAN
rs1801898	MAEL	cis	parietal	SCAN
rs1801898	CYB5R2	trans	lymphoblastoid	seeQTL
rs1801898	PIGC	cis	parietal	SCAN

Chromatin state (count:126 , 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	chr1:171752200-171766600	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:171752200-171767400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:171752200-171768200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr1:171752400-171766600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:171752400-171767200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:171752600-171767000	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:171752600-171767000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:171752600-171767400	Strong transcription	Primary B cells from cord blood	blood
11	chr1:171752600-171767400	Strong transcription	A549	lung
12	chr1:171752600-171767800	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr1:171752600-171767800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:171752800-171766600	Strong transcription	Placenta	Placenta
15	chr1:171752800-171767200	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr1:171752800-171770200	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr1:171753000-171766200	Strong transcription	Brain Substantia Nigra	brain
18	chr1:171753000-171766800	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr1:171753000-171766800	Strong transcription	Brain Hippocampus Middle	brain
20	chr1:171753000-171767200	Strong transcription	Fetal Lung	lung
21	chr1:171753000-171767600	Strong transcription	Fetal Intestine Large	intestine
22	chr1:171753600-171767800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:171754000-171767200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:171754000-171767600	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:171754000-171767800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:171754000-171767800	Strong transcription	Thymus	Thymus
27	chr1:171754200-171766600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:171754200-171767000	Strong transcription	Brain Angular Gyrus	brain
29	chr1:171754200-171767800	Strong transcription	Brain Anterior Caudate	brain
30	chr1:171754200-171767800	Strong transcription	Brain Germinal Matrix	brain
31	chr1:171754200-171768000	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:171754200-171768000	Strong transcription	Fetal Muscle Leg	muscle
33	chr1:171754200-171769600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:171754200-171770200	Strong transcription	Primary T cells from cord blood	blood
35	chr1:171754200-171770200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr1:171754400-171766600	Strong transcription	HepG2	liver
37	chr1:171754400-171767800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:171754400-171768200	Strong transcription	Left Ventricle	heart
39	chr1:171754600-171767400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr1:171754600-171767600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:171754600-171767800	Strong transcription	Primary hematopoietic stem cells	blood
42	chr1:171754600-171768000	Strong transcription	Liver	Liver
43	chr1:171754800-171767400	Strong transcription	Fetal Brain Female	brain
44	chr1:171754800-171767800	Strong transcription	Duodenum Mucosa	Duodenum
45	chr1:171754800-171768200	Strong transcription	Fetal Thymus	thymus
46	chr1:171754800-171768600	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr1:171754800-171768800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:171755000-171766000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:171755000-171767400	Strong transcription	Dnd41	blood
50	chr1:171755000-171767800	Strong transcription	Gastric	stomach

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