Variant report

Variant	rs2814470
Chromosome Location	chr1:165739655-165739656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:165736624-165740514	K562	blood:	n/a	n/a
2	POLR2A	chr1:165737397-165740059	GM12891	blood:	n/a	n/a
3	TBL1XR1	chr1:165739621-165739735	K562	blood:	n/a	n/a
4	POLR2A	chr1:165739459-165740247	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:165737308-165740172	IMR90	lung:	n/a	n/a
6	RFX5	chr1:165739607-165739754	K562	blood:	n/a	n/a
7	POLR2A	chr1:165739624-165739990	GM12878	blood:	n/a	n/a
8	ZC3H11A	chr1:165739637-165739905	K562	blood:	n/a	n/a
9	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
ENSG00000238923	Chromatin interaction
ENSG00000215838	Chromatin interaction
ENSG00000143149	Chromatin interaction
ENSG00000143183	Chromatin interaction
ENSG00000111678	Chromatin interaction
ENSG00000143179	Chromatin interaction
ENSG00000272173	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10800152	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs10918266	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10918276	0.94[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];0.86[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10918281	0.90[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs12028087	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12723198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs14223	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1913846	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2153263	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs2153264	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs2790057	0.81[JPT][hapmap]
rs4656462	0.90[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs4657470	0.88[CEU][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs6426937	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6426940	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6656194	0.80[CHB][hapmap]
rs6670705	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7411708	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7512095	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7540840	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[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
rs2814470	ARHGAP30	cis	parietal	SCAN
rs2814470	TMCO1	cis	brain	BrainEAC
rs2814470	ADCY10	cis	parietal	SCAN
rs2814470	FCGR3A	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165737400-165740200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:165737600-165740000	Active TSS	GM12878-XiMat	blood
3	chr1:165738600-165739800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:165738800-165739800	Flanking Active TSS	Duodenum Mucosa	Duodenum
5	chr1:165738800-165744800	Weak transcription	Spleen	Spleen
6	chr1:165738800-165745200	Weak transcription	Gastric	stomach
7	chr1:165739000-165739800	Enhancers	Placenta Amnion	Placenta Amnion
8	chr1:165739000-165745000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:165739000-165745200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:165739200-165739800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:165739200-165739800	Enhancers	HSMMtube	muscle
12	chr1:165739200-165739800	Enhancers	NHEK	skin
13	chr1:165739200-165740000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:165739200-165740000	Enhancers	Fetal Heart	heart
15	chr1:165739200-165740000	Weak transcription	Ovary	ovary
16	chr1:165739200-165740200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr1:165739200-165740200	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr1:165739200-165740200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:165739200-165740200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:165739200-165740200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:165739200-165740200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:165739200-165740200	Enhancers	Liver	Liver
23	chr1:165739200-165740200	Enhancers	Brain Hippocampus Middle	brain
24	chr1:165739200-165740200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:165739200-165740200	Enhancers	NH-A	brain
26	chr1:165739200-165741200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:165739200-165742600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:165739200-165742600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:165739200-165742800	Weak transcription	Brain Angular Gyrus	brain
30	chr1:165739200-165742800	Weak transcription	Fetal Stomach	stomach
31	chr1:165739200-165743200	Weak transcription	Brain Germinal Matrix	brain
32	chr1:165739200-165743200	Weak transcription	Placenta	Placenta
33	chr1:165739200-165743200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:165739200-165743200	Weak transcription	Thymus	Thymus
35	chr1:165739200-165744600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:165739200-165744800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:165739200-165745200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:165739200-165745400	Weak transcription	Brain Anterior Caudate	brain
39	chr1:165739200-165745400	Weak transcription	Right Ventricle	heart
40	chr1:165739200-165745600	Weak transcription	Fetal Intestine Small	intestine
41	chr1:165739200-165745600	Weak transcription	Lung	lung
42	chr1:165739200-165746000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:165739400-165739800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:165739400-165739800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:165739400-165739800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:165739400-165739800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr1:165739400-165740000	Enhancers	HMEC	breast
48	chr1:165739400-165740200	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr1:165739400-165740200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:165739400-165740200	Enhancers	Duodenum Smooth Muscle	Duodenum

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