Variant report

Variant	rs2936041
Chromosome Location	chr1:222762773-222762774
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	GABPA	chr1:222762696-222764061	SK-N-SH	brain:	n/a	n/a
2	SIN3AK20	chr1:222762584-222763738	HCT-116	colon:	n/a	n/a
3	BHLHE40	chr1:222762671-222763916	K562	blood:	n/a	n/a
4	USF1	chr1:222762685-222763239	SK-N-SH_RA	brain:	n/a	n/a
5	POLR2A	chr1:222762772-222763588	Raji	blood:	n/a	n/a
6	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
7	NR2F2	chr1:222762256-222763834	K562	blood:	n/a	n/a
8	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
9	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
10	MAX	chr1:222762641-222763527	H1-hESC	embryonic stem cell:	n/a	chr1:222762832-222762841 chr1:222762834-222762841 chr1:222762906-222762915 chr1:222762828-222762843 chr1:222762831-222762842 chr1:222762830-222762843 chr1:222762833-222762842
11	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
12	GABPA	chr1:222762714-222763919	A549	lung:	n/a	n/a
13	HCFC1	chr1:222762363-222763705	K562	blood:	n/a	n/a
14	USF1	chr1:222762615-222763330	H1-hESC	embryonic stem cell:	n/a	n/a
15	ELF1	chr1:222762726-222763810	HCT-116	colon:	n/a	n/a
16	ELK4	chr1:222762770-222763411	Hela-S3	cervix:	n/a	n/a
17	MXI1	chr1:222762724-222763582	HepG2	liver:	n/a	chr1:222762906-222762921 chr1:222762904-222762919
18	MAX	chr1:222762697-222763652	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
19	TEAD4	chr1:222762708-222763676	K562	blood:	n/a	n/a
20	MXI1	chr1:222762447-222763810	K562	blood:	n/a	chr1:222762906-222762921 chr1:222762904-222762919
21	SIN3A	chr1:222762546-222763941	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr1:222762733-222763681	GM18505	blood:	n/a	n/a
23	USF1	chr1:222762540-222763301	K562	blood:	n/a	n/a
24	SIN3AK20	chr1:222762714-222763604	H1-hESC	embryonic stem cell:	n/a	n/a
25	MXI1	chr1:222762528-222763896	GM12878	blood:	n/a	chr1:222762906-222762921 chr1:222762904-222762919
26	REST	chr1:222762706-222763776	A549	lung:	n/a	n/a
27	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
28	USF2	chr1:222762689-222763538	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr1:222762420-222764072	GM12891	blood:	n/a	n/a
30	E2F4	chr1:222762749-222763953	MCF10A-Er-Src	breast:	n/a	n/a
31	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
32	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
33	MXI1	chr1:222762686-222763547	H1-hESC	embryonic stem cell:	n/a	chr1:222762906-222762921 chr1:222762904-222762919
34	SIN3AK20	chr1:222762756-222763464	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:222762758-222763619	K562	blood:	n/a	n/a
36	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
37	POLR2A	chr1:222762751-222763620	HepG2	liver:	n/a	n/a
38	POLR2A	chr1:222762584-222764075	MCF10A-Er-Src	breast:	n/a	n/a
39	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
40	MXI1	chr1:222762408-222764085	IMR90	lung:	n/a	chr1:222762906-222762921 chr1:222762904-222762919
41	POLR2A	chr1:222762405-222763763	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr1:222762716-222763728	PFSK-1	brain:	n/a	n/a
43	TCF12	chr1:222762585-222763727	A549	lung:	n/a	n/a
44	USF1	chr1:222762750-222762970	SK-N-SH_RA	brain:	n/a	n/a
45	CUX1	chr1:222762587-222763731	K562	blood:	n/a	n/a
46	POLR2A	chr1:222762581-222764026	GM12878	blood:	n/a	n/a
47	MAX	chr1:222762604-222763732	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
48	RCOR1	chr1:222762343-222763862	K562	blood:	n/a	n/a
49	MYC	chr1:222762682-222763685	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
50	IRF1	chr1:222762658-222763699	K562	blood:	n/a	chr1:222762938-222762958 chr1:222762939-222762952 chr1:222762940-222762954 chr1:222762939-222762952 chr1:222762939-222762950 chr1:222762939-222762952

No.	Distal block	Cell Line	Cell type
1	chr1:222762024..222764722-chr1:222816738..222818394,2	MCF-7	breast:
2	chr1:222761959..222766700-chr1:222790061..222794365,7	MCF-7	breast:
3	chr1:222762075..222764721-chr1:222883311..222887470,5	K562	blood:
4	chr1:222760074..222764679-chr1:222790714..222794830,7	K562	blood:
5	chr1:222760324..222764721-chr1:222884429..222887789,6	K562	blood:
6	chr1:222761567..222764879-chr1:222790132..222793494,4	MCF-7	breast:
7	chr1:222761198..222763394-chr1:222816241..222819069,2	K562	blood:
8	chr1:222760723..222765796-chr1:222790714..222795393,9	K562	blood:

Variant related genes	Relation type
ENSG00000225265	TF binding region
ENSG00000162819	Chromatin interaction
ENSG00000154305	Chromatin interaction
ENSG00000186063	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1024065	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10495194	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10495200	1.00[JPT][hapmap]
rs17463740	0.93[EUR][1000 genomes]
rs17464857	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17511318	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1909194	0.90[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1982983	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2006790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936030	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936044	0.89[EUR][1000 genomes]
rs2936045	0.89[EUR][1000 genomes]
rs2936046	0.89[EUR][1000 genomes]
rs3002130	0.80[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3008594	0.90[CEU][hapmap];0.85[TSI][hapmap]
rs3008645	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3008647	0.80[ASW][hapmap];0.81[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008653	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[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]
rs3008654	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3008655	0.87[EUR][1000 genomes]
rs35750438	0.93[EUR][1000 genomes]
rs3748625	0.97[ASN][1000 genomes]
rs3828060	0.97[ASN][1000 genomes]
rs4328077	0.91[EUR][1000 genomes]
rs73122816	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73122823	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73122834	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73122837	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73122849	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73122850	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73122857	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs74145503	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs74148133	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74148140	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74148142	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9441828	1.00[CEU][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs9441911	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv1842070	chr1:222732027-222763235	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222761600-222762800	Flanking Active TSS	Dnd41	blood
2	chr1:222761600-222763800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:222761800-222763000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr1:222761800-222763000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:222761800-222763800	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:222761800-222764200	Active TSS	H1 Cell Line	embryonic stem cell
7	chr1:222761800-222764200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:222761800-222764200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr1:222761800-222764200	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr1:222761800-222764600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:222762000-222763000	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr1:222762000-222763600	Active TSS	HMEC	breast
13	chr1:222762000-222763600	Active TSS	K562	blood
14	chr1:222762000-222764000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:222762000-222764200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:222762000-222764200	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr1:222762200-222762800	Flanking Active TSS	Brain Cingulate Gyrus	brain
18	chr1:222762200-222762800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
19	chr1:222762200-222762800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:222762200-222762800	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr1:222762200-222762800	Flanking Active TSS	Fetal Heart	heart
22	chr1:222762200-222762800	Flanking Active TSS	Fetal Intestine Small	intestine
23	chr1:222762200-222762800	Flanking Active TSS	Fetal Lung	lung
24	chr1:222762200-222762800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr1:222762200-222762800	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr1:222762200-222762800	Flanking Active TSS	Osteobl	bone
27	chr1:222762200-222763000	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr1:222762200-222763000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr1:222762200-222763200	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr1:222762200-222763400	Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr1:222762200-222763600	Active TSS	Muscle Satellite Cultured Cells	--
32	chr1:222762200-222763600	Active TSS	Stomach Mucosa	stomach
33	chr1:222762200-222763600	Active TSS	NHEK	skin
34	chr1:222762200-222763800	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr1:222762200-222763800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr1:222762200-222763800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:222762200-222763800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:222762200-222763800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:222762200-222763800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:222762200-222763800	Active TSS	A549	lung
41	chr1:222762200-222764000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:222762200-222764000	Active TSS	Ovary	ovary
43	chr1:222762200-222764200	Active TSS	H9 Cell Line	embryonic stem cell
44	chr1:222762200-222764200	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr1:222762200-222764200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:222762400-222762800	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr1:222762400-222762800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr1:222762400-222762800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr1:222762400-222762800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr1:222762400-222762800	Flanking Active TSS	Brain Substantia Nigra	brain

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