Variant report

Variant	rs360103
Chromosome Location	chr1:226068927-226068928
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	RUNX3	chr1:226068804-226069179	GM12878	blood:	n/a	n/a
2	ZBTB7A	chr1:226068784-226070952	K562	blood:	n/a	chr1:226070384-226070395
3	POLR2A	chr1:226068736-226069211	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr1:226068788-226068976	MCF10A-Er-Src	breast:	n/a	n/a
5	NR2F2	chr1:226068421-226070907	K562	blood:	n/a	n/a
6	ZNF263	chr1:226068002-226069049	HEK293-T-REx	kidney:	n/a	chr1:226068130-226068151
7	FOS	chr1:226068704-226069045	MCF10A-Er-Src	breast:	n/a	chr1:226068889-226068900 chr1:226068852-226068861
8	STAT3	chr1:226068843-226069104	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:226068894-226071165	H1-hESC	embryonic stem cell:	n/a	n/a
10	MTA3	chr1:226068766-226071109	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:226068828-226069042	K562	blood:	n/a	n/a
12	MXI1	chr1:226068728-226071124	IMR90	lung:	n/a	chr1:226069159-226069168 chr1:226070774-226070789
13	POLR2A	chr1:226068924-226069000	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr1:226068783-226069072	K562	blood:	n/a	n/a
15	CTCF	chr1:226068820-226068970	GM12874	blood:	n/a	n/a
16	CTCF	chr1:226068840-226068990	GM12872	blood:	n/a	n/a
17	FOS	chr1:226068725-226068956	MCF10A-Er-Src	breast:	n/a	chr1:226068889-226068900 chr1:226068852-226068861
18	ELF1	chr1:226068758-226069068	K562	blood:	n/a	n/a
19	POLR2A	chr1:226068622-226069093	MCF10A-Er-Src	breast:	n/a	n/a
20	FOS	chr1:226068749-226068937	MCF10A-Er-Src	breast:	n/a	chr1:226068889-226068900 chr1:226068852-226068861
21	STAT3	chr1:226068857-226068951	MCF10A-Er-Src	breast:	n/a	n/a
22	MYC	chr1:226068839-226068932	MCF10A-Er-Src	breast:	n/a	n/a
23	MAX	chr1:226068669-226071124	K562	blood:	n/a	chr1:226070644-226070654
24	POLR2A	chr1:226068926-226071280	HepG2	liver:	n/a	n/a
25	POLR2A	chr1:226068032-226070946	HepG2	liver:	n/a	n/a
26	SMARCB1	chr1:226068859-226071062	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:226068819-226071009	K562	blood:	n/a	n/a
28	ZNF263	chr1:226068881-226070974	K562	blood:	n/a	n/a
29	MAZ	chr1:226068907-226070980	K562	blood:	n/a	chr1:226070644-226070654
30	SIN3A	chr1:226068736-226070555	H1-hESC	embryonic stem cell:	n/a	chr1:226070229-226070240
31	POLR2A	chr1:226068700-226070621	IMR90	lung:	n/a	n/a

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	chr1:225964533..225968744-chr1:226068261..226071590,3	MCF-7	breast:
4	chr1:226035721..226038687-chr1:226067702..226069898,2	K562	blood:
5	chr1:226068530..226073051-chr1:226075073..226079547,5	MCF-7	breast:
6	chr1:226047047..226048850-chr1:226067848..226071913,3	MCF-7	breast:
7	chr1:226067837..226071624-chr1:226184531..226189088,6	K562	blood:
8	chr1:45272119..45273039-chr1:226068246..226068993,2	Hela-S3	cervix:
9	chr1:226067837..226069575-chr1:226185536..226187793,2	K562	blood:
10	chr1:226066440..226072029-chr1:226106315..226113044,10	MCF-7	breast:
11	chr1:226067470..226074101-chr1:226108823..226116408,13	MCF-7	breast:
12	chr1:226066914..226069709-chr1:226309865..226312651,2	K562	blood:

Variant related genes	Relation type
TMEM63A	TF binding region
ENSG00000143742	Chromatin interaction
ENSG00000196187	Chromatin interaction
ENSG00000143811	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000243709	Chromatin interaction
ENSG00000188396	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs111990	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12041277	0.85[ASN][1000 genomes]
rs1223246	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs1237433	0.82[EUR][1000 genomes]
rs168618	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs168619	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs360061	0.83[ASN][1000 genomes]
rs360063	0.90[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs360074	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs360075	0.86[EUR][1000 genomes]
rs360077	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs360083	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs360088	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360091	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs360092	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360093	1.00[ASW][hapmap];0.87[CEU][hapmap];0.81[LWK][hapmap];0.89[MKK][hapmap];0.82[AFR][1000 genomes]
rs360094	1.00[ASW][hapmap];0.83[CEU][hapmap];0.91[MKK][hapmap];0.82[AFR][1000 genomes]
rs360095	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs360096	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs360097	1.00[ASW][hapmap];0.83[CEU][hapmap];0.91[MKK][hapmap];0.82[AFR][1000 genomes]
rs360098	0.83[CEU][hapmap]
rs360100	0.82[AFR][1000 genomes]
rs360101	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.87[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]
rs360102	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]

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
rs360103	TMEM63A	cis	parietal	SCAN
rs360103	TMEM63A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226065000-226069200	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr1:226065200-226069000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:226065400-226069000	Enhancers	Brain Angular Gyrus	brain
4	chr1:226065400-226069400	Flanking Active TSS	Duodenum Mucosa	Duodenum
5	chr1:226065600-226069000	Enhancers	Small Intestine	intestine
6	chr1:226065800-226069000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:226066400-226069000	Enhancers	Placenta	Placenta
8	chr1:226066400-226069200	Enhancers	Spleen	Spleen
9	chr1:226066400-226070000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:226066600-226069000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:226066600-226069000	Enhancers	Esophagus	oesophagus
12	chr1:226066600-226069400	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr1:226066600-226069400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr1:226066800-226069000	Enhancers	Fetal Muscle Trunk	muscle
15	chr1:226066800-226069400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr1:226067000-226069200	Weak transcription	Ovary	ovary
17	chr1:226067000-226069400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr1:226067000-226069600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr1:226067000-226070000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:226067200-226069200	Flanking Active TSS	HepG2	liver
21	chr1:226067200-226069400	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr1:226067200-226069400	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr1:226067200-226069800	Flanking Active TSS	Fetal Thymus	thymus
24	chr1:226067200-226070000	Flanking Active TSS	Dnd41	blood
25	chr1:226067200-226071000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:226067400-226069200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:226067400-226069400	Flanking Active TSS	Rectal Smooth Muscle	rectum
28	chr1:226067400-226069600	Flanking Active TSS	Liver	Liver
29	chr1:226067400-226069800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:226067600-226069400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr1:226067600-226069600	Enhancers	Fetal Heart	heart
32	chr1:226067800-226069000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr1:226067800-226069200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr1:226067800-226069400	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr1:226067800-226069400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr1:226067800-226069400	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr1:226067800-226069400	Flanking Active TSS	Fetal Intestine Large	intestine
38	chr1:226067800-226069400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr1:226067800-226069400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr1:226067800-226069400	Flanking Active TSS	GM12878-XiMat	blood
41	chr1:226067800-226069600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr1:226067800-226069600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:226067800-226070000	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr1:226067800-226070000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr1:226068000-226069000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:226068000-226069000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:226068000-226069000	Transcr. at gene 5' and 3'	K562	blood
48	chr1:226068000-226069200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:226068000-226069400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr1:226068000-226069400	Flanking Active TSS	Fetal Lung	lung

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