Variant report

Variant	rs2814471
Chromosome Location	chr1:165739598-165739599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:165737551-165739622	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:165736624-165740514	K562	blood:	n/a	n/a
3	POLR2A	chr1:165737397-165740059	GM12891	blood:	n/a	n/a
4	POLR2A	chr1:165739010-165739623	K562	blood:	n/a	n/a
5	POLR2A	chr1:165739459-165740247	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:165737308-165740172	IMR90	lung:	n/a	n/a
7	MAFF	chr1:165739519-165739685	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:165735886..165744990-chr1:165791702..165805629,42	K562	blood:
2	chr1:165739180..165741043-chr1:165759339..165761023,2	MCF-7	breast:
3	chr1:165736523..165741866-chr1:165791420..165802380,26	K562	blood:
4	chr1:165736117..165742504-chr1:165795129..165799551,11	MCF-7	breast:
5	chr1:165735066..165739781-chr1:165794447..165799093,13	MCF-7	breast:
6	chr1:165737601..165739848-chr12:7052889..7054535,2	MCF-7	breast:
7	chr1:165667536..165669486-chr1:165736821..165739691,4	MCF-7	breast:

No data

Variant related genes	Relation type
TMCO1	TF binding region
ENSG00000143183	Chromatin interaction
ENSG00000143179	Chromatin interaction
ENSG00000272173	Chromatin interaction
ENSG00000238923	Chromatin interaction
ENSG00000111678	Chromatin interaction
ENSG00000215838	Chromatin interaction
ENSG00000143149	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10800135	1.00[JPT][hapmap]
rs10800153	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800154	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10800155	1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918274	0.94[EUR][1000 genomes]
rs12133745	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403369	1.00[JPT][hapmap]
rs12691499	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12691500	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547725	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs2251768	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2790049	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790052	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790053	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814463	0.83[ASN][1000 genomes]
rs2814466	1.00[JPT][hapmap]
rs28504591	0.80[EUR][1000 genomes]
rs4233408	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4537525	1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4603103	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656461	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657471	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4657472	0.83[ASN][1000 genomes]
rs4657474	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4657475	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657476	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657477	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660601	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662839	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668108	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668885	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6696454	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71628393	0.83[ASN][1000 genomes]
rs7518099	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524755	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7528177	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7555523	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[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	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv518886	chr1:165714187-165741646	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2814471	ADCY10	cis	parietal	SCAN
rs2814471	NDUFS2	cis	cerebellum	SCAN
rs2814471	ARHGAP30	cis	parietal	SCAN
rs2814471	MAEL	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165737200-165739600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:165737400-165740200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:165737600-165739600	Active TSS	HSMM	muscle
4	chr1:165737600-165739600	Active TSS	NHLF	lung
5	chr1:165737600-165740000	Active TSS	GM12878-XiMat	blood
6	chr1:165738400-165739600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:165738600-165739600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr1:165738600-165739600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr1:165738600-165739600	Flanking Active TSS	Dnd41	blood
10	chr1:165738600-165739800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:165738800-165739600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:165738800-165739600	Enhancers	Pancreas	Pancrea
13	chr1:165738800-165739600	Flanking Active TSS	Hela-S3	cervix
14	chr1:165738800-165739800	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr1:165738800-165744800	Weak transcription	Spleen	Spleen
16	chr1:165738800-165745200	Weak transcription	Gastric	stomach
17	chr1:165739000-165739600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:165739000-165739600	Enhancers	Primary B cells from peripheral blood	blood
19	chr1:165739000-165739600	Enhancers	Primary T cells fromperipheralblood	blood
20	chr1:165739000-165739600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:165739000-165739600	Enhancers	Fetal Brain Male	brain
22	chr1:165739000-165739600	Enhancers	Fetal Thymus	thymus
23	chr1:165739000-165739600	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr1:165739000-165739800	Enhancers	Placenta Amnion	Placenta Amnion
25	chr1:165739000-165745000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:165739000-165745200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:165739200-165739600	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr1:165739200-165739600	Enhancers	Primary T cells from cord blood	blood
29	chr1:165739200-165739600	Enhancers	Primary hematopoietic stem cells	blood
30	chr1:165739200-165739600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr1:165739200-165739600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:165739200-165739600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:165739200-165739600	Enhancers	Adipose Nuclei	Adipose
34	chr1:165739200-165739600	Enhancers	Fetal Muscle Trunk	muscle
35	chr1:165739200-165739600	Enhancers	Fetal Muscle Leg	muscle
36	chr1:165739200-165739600	Enhancers	Stomach Mucosa	stomach
37	chr1:165739200-165739600	Flanking Active TSS	HepG2	liver
38	chr1:165739200-165739600	Enhancers	HUVEC	blood vessel
39	chr1:165739200-165739600	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr1:165739200-165739800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr1:165739200-165739800	Enhancers	HSMMtube	muscle
42	chr1:165739200-165739800	Enhancers	NHEK	skin
43	chr1:165739200-165740000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:165739200-165740000	Enhancers	Fetal Heart	heart
45	chr1:165739200-165740000	Weak transcription	Ovary	ovary
46	chr1:165739200-165740200	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr1:165739200-165740200	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr1:165739200-165740200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:165739200-165740200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:165739200-165740200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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