Variant report

Variant	rs2232816
Chromosome Location	chr1:171753039-171753040
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	POLR2A	chr1:171753001-171753041	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:171749779..171754190-chr1:171762974..171767849,5	K562	blood:
2	chr1:171709343..171715185-chr1:171748592..171756289,15	K562	blood:
3	chr1:171752566..171754106-chr1:171760621..171762669,2	MCF-7	breast:

Variant related genes	Relation type
METTL13	TF binding region
ENSG00000010165	Chromatin interaction
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10489253	0.86[YRI][hapmap]
rs10798634	0.84[EUR][1000 genomes]
rs10798636	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10798667	0.92[ASN][1000 genomes]
rs10798692	0.83[MEX][hapmap]
rs10913644	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11587288	0.94[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11590059	0.83[AFR][1000 genomes]
rs11803889	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs12022693	0.83[AFR][1000 genomes]
rs12028128	0.84[EUR][1000 genomes]
rs12032340	0.82[MEX][hapmap];0.84[EUR][1000 genomes]
rs12034454	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039034	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12566700	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.93[ASN][1000 genomes]
rs16843385	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17597528	0.83[AFR][1000 genomes]
rs2206541	0.86[YRI][hapmap]
rs2232812	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2232818	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232826	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294723	0.83[MEX][hapmap]
rs3753538	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56167663	0.86[AFR][1000 genomes]
rs56178029	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57476157	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59302445	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60502293	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60956160	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6425405	0.84[EUR][1000 genomes]
rs6425423	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425428	0.83[AFR][1000 genomes]
rs6425438	0.87[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs6425439	0.91[ASN][1000 genomes]
rs6684594	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6690544	0.83[YRI][hapmap]
rs6691222	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6692136	0.84[EUR][1000 genomes]
rs6695502	0.88[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6700184	0.89[YRI][hapmap]
rs72703115	0.92[ASN][1000 genomes]
rs7537770	0.86[YRI][hapmap]
rs7541192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7542116	0.84[EUR][1000 genomes]
rs7543608	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7548462	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7551037	0.83[EUR][1000 genomes]
rs7556602	0.89[YRI][hapmap]
rs7860	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs909958	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs941942	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][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	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
4	nsv522889	chr1:171749665-171755071	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv518222	chr1:171753039-171763549	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2232816	DCAF6	cis	cerebellum	SCAN
rs2232816	BAT2L2	cis	parietal	SCAN
rs2232816	DNM3	cis	cerebellum	SCAN
rs2232816	MAEL	cis	parietal	SCAN
rs2232816	METTL13	cis	parietal	SCAN
rs2232816	VAMP4	cis	parietal	SCAN
rs2232816	DUSP27	cis	cerebellum	SCAN
rs2232816	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171751400-171754400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr1:171751400-171755000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:171751600-171754800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:171751600-171770800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:171751800-171753200	Enhancers	Pancreas	Pancrea
6	chr1:171751800-171754200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:171752000-171754600	Weak transcription	HSMMtube	muscle
8	chr1:171752000-171754800	Weak transcription	Small Intestine	intestine
9	chr1:171752000-171755000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:171752000-171773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:171752200-171753400	Weak transcription	Stomach Mucosa	stomach
12	chr1:171752200-171753600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:171752200-171753600	Weak transcription	Fetal Brain Male	brain
14	chr1:171752200-171753800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr1:171752200-171753800	Weak transcription	NH-A	brain
16	chr1:171752200-171753800	Weak transcription	NHDF-Ad	bronchial
17	chr1:171752200-171755000	Weak transcription	Osteobl	bone
18	chr1:171752200-171759200	Weak transcription	Fetal Heart	heart
19	chr1:171752200-171762200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:171752200-171766600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:171752200-171767400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:171752200-171768200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:171752400-171753400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:171752400-171753400	Enhancers	Hela-S3	cervix
25	chr1:171752400-171753400	Genic enhancers	NHLF	lung
26	chr1:171752400-171753800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr1:171752400-171753800	Strong transcription	Fetal Muscle Leg	muscle
28	chr1:171752400-171754000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:171752400-171754000	Genic enhancers	HMEC	breast
30	chr1:171752400-171754200	Transcr. at gene 5' and 3'	Dnd41	blood
31	chr1:171752400-171754400	Weak transcription	Fetal Kidney	kidney
32	chr1:171752400-171754800	Genic enhancers	Duodenum Mucosa	Duodenum
33	chr1:171752400-171754800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:171752400-171754800	Weak transcription	HUVEC	blood vessel
35	chr1:171752400-171755400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:171752400-171755400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:171752400-171755400	Genic enhancers	K562	blood
38	chr1:171752400-171755600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:171752400-171766600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:171752400-171767200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:171752600-171753800	Strong transcription	Brain Anterior Caudate	brain
42	chr1:171752600-171754000	Strong transcription	Fetal Thymus	thymus
43	chr1:171752600-171754200	Genic enhancers	Primary T cells from cord blood	blood
44	chr1:171752600-171754200	Genic enhancers	Brain Angular Gyrus	brain
45	chr1:171752600-171754600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr1:171752600-171754600	Genic enhancers	Liver	Liver
47	chr1:171752600-171754600	Strong transcription	HSMM	muscle
48	chr1:171752600-171755000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr1:171752600-171755200	Genic enhancers	Stomach Smooth Muscle	stomach
50	chr1:171752600-171755600	Genic enhancers	Skeletal Muscle Female	skeletal muscle

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