Variant report

Variant	rs2936040
Chromosome Location	chr1:222763661-222763662
allele	A/T
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	chr1:222762884-222764007	GM15510	blood:	n/a	n/a
2	GABPA	chr1:222762696-222764061	SK-N-SH	brain:	n/a	n/a
3	SIN3AK20	chr1:222762584-222763738	HCT-116	colon:	n/a	n/a
4	BHLHE40	chr1:222762671-222763916	K562	blood:	n/a	n/a
5	CBX3	chr1:222762863-222764109	K562	blood:	n/a	n/a
6	RELA	chr1:222762913-222763772	GM19099	blood:	n/a	n/a
7	POLR2A	chr1:222762830-222763714	U87	brain:	n/a	n/a
8	MAX	chr1:222762705-222763912	HepG2	liver:	n/a	chr1:222762832-222762841 chr1:222762834-222762841 chr1:222762906-222762915 chr1:222762828-222762843 chr1:222762831-222762842 chr1:222762830-222762843 chr1:222762833-222762842
9	NR2F2	chr1:222762256-222763834	K562	blood:	n/a	n/a
10	POLR2A	chr1:222762775-222763914	MCF10A-Er-Src	breast:	n/a	n/a
11	MAX	chr1:222762509-222763726	HCT-116	colon:	n/a	chr1:222762832-222762841 chr1:222762834-222762841 chr1:222762906-222762915 chr1:222762828-222762843 chr1:222762831-222762842 chr1:222762830-222762843 chr1:222762833-222762842
12	MAX	chr1:222762679-222763724	ECC-1	luminal epithelium:	n/a	chr1:222762832-222762841 chr1:222762834-222762841 chr1:222762906-222762915 chr1:222762828-222762843 chr1:222762831-222762842 chr1:222762830-222762843 chr1:222762833-222762842
13	STAT5A	chr1:222762881-222763818	K562	blood:	n/a	chr1:222762939-222762950 chr1:222763010-222763022
14	GABPA	chr1:222762810-222763765	MCF-7	breast:	n/a	n/a
15	GABPA	chr1:222762810-222763778	SK-N-SH	brain:	n/a	n/a
16	MYC	chr1:222762223-222763947	K562	blood:	n/a	chr1:222762832-222762841 chr1:222762834-222762841 chr1:222762906-222762915 chr1:222762828-222762843 chr1:222762831-222762842 chr1:222762830-222762843 chr1:222762833-222762842
17	GABPA	chr1:222762714-222763919	A549	lung:	n/a	n/a
18	HCFC1	chr1:222762363-222763705	K562	blood:	n/a	n/a
19	ELF1	chr1:222762726-222763810	HCT-116	colon:	n/a	n/a
20	GABPA	chr1:222762977-222763732	K562	blood:	n/a	n/a
21	TBL1XR1	chr1:222762967-222763743	K562	blood:	n/a	n/a
22	TEAD4	chr1:222762708-222763676	K562	blood:	n/a	n/a
23	MXI1	chr1:222762447-222763810	K562	blood:	n/a	chr1:222762906-222762921 chr1:222762904-222762919
24	SIN3A	chr1:222762546-222763941	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr1:222762850-222763674	MCF-7	breast:	n/a	n/a
26	POLR2A	chr1:222762733-222763681	GM18505	blood:	n/a	n/a
27	MAFK	chr1:222763110-222763798	HepG2	liver:	n/a	n/a
28	POLR2A	chr1:222762839-222763775	K562	blood:	n/a	n/a
29	TAF1	chr1:222762966-222763661	SK-N-SH	brain:	n/a	n/a
30	MXI1	chr1:222762528-222763896	GM12878	blood:	n/a	chr1:222762906-222762921 chr1:222762904-222762919
31	REST	chr1:222762706-222763776	A549	lung:	n/a	n/a
32	GABPA	chr1:222762959-222763930	K562	blood:	n/a	n/a
33	MAX	chr1:222762709-222763742	MCF-7	breast:	n/a	chr1:222762832-222762841 chr1:222762834-222762841 chr1:222762906-222762915 chr1:222762828-222762843 chr1:222762831-222762842 chr1:222762830-222762843 chr1:222762833-222762842
34	POLR2A	chr1:222762811-222764106	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:222762420-222764072	GM12891	blood:	n/a	n/a
36	ARID3A	chr1:222763003-222763800	HepG2	liver:	n/a	n/a
37	POLR2A	chr1:222762878-222763980	GM12878	blood:	n/a	n/a
38	E2F4	chr1:222762749-222763953	MCF10A-Er-Src	breast:	n/a	n/a
39	TAF1	chr1:222762888-222763671	A549	lung:	n/a	n/a
40	IRF1	chr1:222762495-222763937	K562	blood:	n/a	chr1:222762938-222762958 chr1:222762939-222762952 chr1:222762940-222762954 chr1:222762939-222762952 chr1:222762939-222762950 chr1:222762939-222762952
41	MYC	chr1:222762507-222763733	MCF10A-Er-Src	breast:	n/a	chr1:222762832-222762841 chr1:222762834-222762841 chr1:222762906-222762915 chr1:222762828-222762843 chr1:222762831-222762842 chr1:222762830-222762843 chr1:222762833-222762842
42	POLR2A	chr1:222762788-222764033	GM19099	blood:	n/a	n/a
43	BHLHE40	chr1:222762930-222763679	HepG2	liver:	n/a	n/a
44	RUNX3	chr1:222763014-222763812	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:222762873-222763699	K562	blood:	n/a	n/a
46	MAX	chr1:222762593-222763694	A549	lung:	n/a	chr1:222762832-222762841 chr1:222762834-222762841 chr1:222762906-222762915 chr1:222762828-222762843 chr1:222762831-222762842 chr1:222762830-222762843 chr1:222762833-222762842
47	MAFK	chr1:222763178-222763706	IMR90	lung:	n/a	n/a
48	POLR2A	chr1:222762584-222764075	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr1:222762849-222763799	SK-N-SH	brain:	n/a	n/a
50	MAX	chr1:222762300-222763695	K562	blood:	n/a	chr1:222762832-222762841 chr1:222762834-222762841 chr1:222762906-222762915 chr1:222762828-222762843 chr1:222762831-222762842 chr1:222762830-222762843 chr1:222762833-222762842

No.	Distal block	Cell Line	Cell type
1	chr1:222763603..222766024-chr1:222777146..222778835,2	K562	blood:
2	chr1:222762024..222764722-chr1:222816738..222818394,2	MCF-7	breast:
3	chr1:222762853..222764726-chr1:222816205..222818798,3	MCF-7	breast:
4	chr1:222761959..222766700-chr1:222790061..222794365,7	MCF-7	breast:
5	chr1:222762075..222764721-chr1:222883311..222887470,5	K562	blood:
6	chr1:222760074..222764679-chr1:222790714..222794830,7	K562	blood:
7	chr1:222760324..222764721-chr1:222884429..222887789,6	K562	blood:
8	chr1:222761567..222764879-chr1:222790132..222793494,4	MCF-7	breast:
9	chr1:222759001..222761767-chr1:222763501..222765317,2	MCF-7	breast:
10	chr1:222760723..222765796-chr1:222790714..222795393,9	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MIA3-2	chr1:222763600-222763749	XLOC_000576
2	lnc-MIA3-2	chr1:222763304-222763749	XLOC_000576
3	lnc-TAF1A-1	chr1:222763365-222763742	XLOC_001217
4	lnc-MIA3-2	chr1:222763304-222763749	NONHSAT009690

Variant related genes	Relation type
TAF1A	TF binding region
ENSG00000162819	Chromatin interaction
ENSG00000154305	Chromatin interaction
ENSG00000186063	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11485178	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11485180	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11487813	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1319392	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1603742	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17163214	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1909192	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1995152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133185	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2173401	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2378583	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2936027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936031	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2936034	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2936035	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2936037	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2936038	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2936048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3002151	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3008641	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008644	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4400619	0.96[AMR][1000 genomes];0.91[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	nsv873203	chr1:222332906-222775000	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2936040	GPATCH2	cis	cerebellum	SCAN
rs2936040	LOC400804	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222761600-222763800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:222761800-222763800	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:222761800-222764200	Active TSS	H1 Cell Line	embryonic stem cell
4	chr1:222761800-222764200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:222761800-222764200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:222761800-222764200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:222761800-222764600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:222762000-222764000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:222762000-222764200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:222762000-222764200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr1:222762200-222763800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:222762200-222763800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr1:222762200-222763800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:222762200-222763800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:222762200-222763800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:222762200-222763800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:222762200-222763800	Active TSS	A549	lung
18	chr1:222762200-222764000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:222762200-222764000	Active TSS	Ovary	ovary
20	chr1:222762200-222764200	Active TSS	H9 Cell Line	embryonic stem cell
21	chr1:222762200-222764200	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr1:222762200-222764200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:222762400-222763800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:222762400-222763800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:222762400-222764000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:222762400-222764000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:222762400-222764000	Active TSS	Fetal Muscle Trunk	muscle
28	chr1:222762400-222764000	Active TSS	Right Atrium	heart
29	chr1:222762400-222764200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:222762600-222763800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:222762600-222763800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:222762600-222763800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr1:222762600-222763800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:222762600-222763800	Active TSS	Aorta	Aorta
35	chr1:222762600-222763800	Active TSS	Brain Hippocampus Middle	brain
36	chr1:222762600-222763800	Active TSS	Colon Smooth Muscle	Colon
37	chr1:222762600-222763800	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr1:222762600-222763800	Active TSS	Fetal Kidney	kidney
39	chr1:222762600-222763800	Active TSS	Fetal Muscle Leg	muscle
40	chr1:222762600-222763800	Active TSS	Gastric	stomach
41	chr1:222762600-222763800	Active TSS	Lung	lung
42	chr1:222762600-222763800	Active TSS	Placenta Amnion	Placenta Amnion
43	chr1:222762600-222763800	Active TSS	Right Ventricle	heart
44	chr1:222762600-222763800	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr1:222762600-222763800	Active TSS	Small Intestine	intestine
46	chr1:222762600-222764000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:222762600-222764000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:222762600-222764000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:222762600-222764000	Active TSS	Esophagus	oesophagus
50	chr1:222762600-222764000	Active TSS	Left Ventricle	heart

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