Variant report

Variant	rs360102
Chromosome Location	chr1:226067862-226067863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAL1	chr1:226067754-226067969	K562	blood:	n/a	n/a
2	POLR2A	chr1:226067855-226067923	K562	blood:	n/a	n/a
3	CEBPB	chr1:226067715-226067913	K562	blood:	n/a	chr1:226067772-226067789

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226063406..226070293-chr1:226107715..226112317,7	K562	blood:
2	chr1:226067757..226070388-chr1:226097360..226099727,2	MCF-7	breast:
3	chr1:226035721..226038687-chr1:226067702..226069898,2	K562	blood:
4	chr1:225839309..225842570-chr1:226062972..226068660,6	MCF-7	breast:
5	chr1:226047047..226048850-chr1:226067848..226071913,3	MCF-7	breast:
6	chr1:226067837..226071624-chr1:226184531..226189088,6	K562	blood:
7	chr1:226061864..226068048-chr1:226072871..226078674,7	MCF-7	breast:
8	chr1:226066286..226068064-chr1:226160996..226163119,2	K562	blood:
9	chr1:226066024..226068193-chr1:226076140..226078255,2	MCF-7	breast:
10	chr1:226065700..226068385-chr1:226110654..226114654,4	K562	blood:
11	chr1:226067837..226069575-chr1:226185536..226187793,2	K562	blood:
12	chr1:226066440..226072029-chr1:226106315..226113044,10	MCF-7	breast:
13	chr1:226067470..226074101-chr1:226108823..226116408,13	MCF-7	breast:
14	chr1:226066914..226069709-chr1:226309865..226312651,2	K562	blood:

No data

Variant related genes	Relation type
TMEM63A	TF binding region
ENSG00000143751	Chromatin interaction
ENSG00000143811	Chromatin interaction
ENSG00000196187	Chromatin interaction
ENSG00000243709	Chromatin interaction
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs111990	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12041277	0.88[ASN][1000 genomes]
rs1223246	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs1237433	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs168618	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs168619	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2292563	0.83[CEU][hapmap]
rs2292564	0.83[CEU][hapmap]
rs2854452	0.83[ASN][1000 genomes]
rs360061	0.87[ASN][1000 genomes]
rs360063	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]
rs360074	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs360075	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs360076	0.82[CEU][hapmap]
rs360077	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs360083	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs360088	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs360091	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360092	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs360093	0.88[ASW][hapmap];0.96[CEU][hapmap];0.89[MKK][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes]
rs360094	0.88[ASW][hapmap];0.91[CEU][hapmap];0.90[MKK][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs360095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs360096	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];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs360097	0.88[ASW][hapmap];0.91[CEU][hapmap];0.90[MKK][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs360098	0.91[CEU][hapmap]
rs360100	0.91[AFR][1000 genomes]
rs360101	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[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]
rs360103	0.88[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820236	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv520628	chr1:226026406-226093362	Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs360102	LEFTY1	trans	multi-tissue	Pritchard
rs360102	LEFTY1	cis	Liver	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226050200-226068600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:226059600-226068800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:226060200-226068600	Weak transcription	NH-A	brain
4	chr1:226063000-226068200	Genic enhancers	Fetal Muscle Leg	muscle
5	chr1:226063200-226068200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:226064200-226068000	Weak transcription	NHEK	skin
7	chr1:226064800-226068200	Enhancers	NHDF-Ad	bronchial
8	chr1:226065000-226068000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:226065000-226068800	Enhancers	Left Ventricle	heart
10	chr1:226065000-226068800	Enhancers	Psoas Muscle	Psoas
11	chr1:226065000-226068800	Enhancers	Right Ventricle	heart
12	chr1:226065000-226068800	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr1:226065000-226069200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:226065200-226068200	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr1:226065200-226068600	Enhancers	Aorta	Aorta
16	chr1:226065200-226068800	Enhancers	Right Atrium	heart
17	chr1:226065200-226069000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:226065400-226068000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:226065400-226068000	Enhancers	Stomach Mucosa	stomach
20	chr1:226065400-226068200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:226065400-226068400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
22	chr1:226065400-226068600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:226065400-226069000	Enhancers	Brain Angular Gyrus	brain
24	chr1:226065400-226069400	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr1:226065600-226068000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:226065600-226068000	Weak transcription	Hela-S3	cervix
27	chr1:226065600-226068000	Genic enhancers	K562	blood
28	chr1:226065600-226068800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr1:226065600-226069000	Enhancers	Small Intestine	intestine
30	chr1:226065800-226068000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:226065800-226068000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:226065800-226068200	Enhancers	Colon Smooth Muscle	Colon
33	chr1:226065800-226068200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:226065800-226068800	Enhancers	Lung	lung
35	chr1:226065800-226069000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:226066000-226068000	Weak transcription	HSMM	muscle
37	chr1:226066000-226068200	Weak transcription	HSMMtube	muscle
38	chr1:226066400-226069000	Enhancers	Placenta	Placenta
39	chr1:226066400-226069200	Enhancers	Spleen	Spleen
40	chr1:226066400-226070000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:226066600-226068000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:226066600-226068000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
43	chr1:226066600-226068200	Weak transcription	Fetal Kidney	kidney
44	chr1:226066600-226068600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:226066600-226068600	Weak transcription	HUVEC	blood vessel
46	chr1:226066600-226068800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:226066600-226069000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr1:226066600-226069000	Enhancers	Esophagus	oesophagus
49	chr1:226066600-226069400	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr1:226066600-226069400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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