Variant report

Variant	rs11801772
Chromosome Location	chr1:197169795-197169796
allele	C/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	POLR2A	chr1:197169459-197171065	ProgFib	skin:	n/a	n/a
2	RUNX3	chr1:197169722-197170982	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:197169708-197171333	K562	blood:	n/a	n/a
4	RCOR1	chr1:197169457-197171496	Hela-S3	cervix:	n/a	n/a
5	SIN3A	chr1:197169600-197171402	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:197169189-197171283	GM12878	blood:	n/a	n/a
7	MAX	chr1:197169327-197170912	NB4	blood:	n/a	n/a
8	POLR2A	chr1:197169405-197171351	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:197169746-197170984	HUVEC	blood vessel:	n/a	n/a
10	MAX	chr1:197169525-197171542	Hela-S3	cervix:	n/a	chr1:197171270-197171280
11	POLR2A	chr1:197169396-197170973	IMR90	lung:	n/a	n/a
12	MAZ	chr1:197169298-197171231	K562	blood:	n/a	n/a
13	SMARCC1	chr1:197169169-197171341	Hela-S3	cervix:	n/a	n/a
14	MAX	chr1:197169746-197170915	K562	blood:	n/a	n/a
15	POLR2A	chr1:197169780-197171004	PBDE	blood:	n/a	n/a
16	SIN3AK20	chr1:197169341-197171230	MCF-7	breast:	n/a	n/a
17	MAX	chr1:197169744-197171006	ECC-1	luminal epithelium:	n/a	n/a
18	EP300	chr1:197169237-197169880	K562	blood:	n/a	n/a
19	REST	chr1:197169624-197171049	H1-neurons	neurons:	n/a	n/a
20	MAX	chr1:197169496-197170909	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr1:197169137-197171515	GM12891	blood:	n/a	n/a
22	GATA3	chr1:197169509-197170147	T-47D	breast:	n/a	n/a
23	TCF7L2	chr1:197169793-197170934	Hela-S3	cervix:	n/a	n/a
24	TEAD4	chr1:197169117-197169955	K562	blood:	n/a	n/a
25	POLR2A	chr1:197169440-197169850	K562	blood:	n/a	n/a
26	TCF12	chr1:197169630-197171208	A549	lung:	n/a	n/a
27	STAT3	chr1:197169703-197169931	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr1:197169394-197171752	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr1:197169483-197171468	SK-N-MC	brain:	n/a	n/a
30	POLR2A	chr1:197169667-197170974	K562	blood:	n/a	n/a
31	POLR2A	chr1:197169625-197170981	GM12892	blood:	n/a	n/a
32	RFX5	chr1:197169337-197171431	Hela-S3	cervix:	n/a	n/a
33	FOS	chr1:197169694-197169909	MCF10A-Er-Src	breast:	n/a	n/a
34	RCOR1	chr1:197169397-197171399	K562	blood:	n/a	n/a
35	POLR2A	chr1:197169568-197170013	K562	blood:	n/a	n/a
36	MYC	chr1:197169638-197170839	MCF10A-Er-Src	breast:	n/a	n/a
37	CCNT2	chr1:197169302-197171216	K562	blood:	n/a	n/a
38	MTA3	chr1:197169685-197171333	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:197169657-197171019	K562	blood:	n/a	n/a
40	PML	chr1:197169569-197171172	GM12878	blood:	n/a	n/a
41	GTF2F1	chr1:197169624-197171340	Hela-S3	cervix:	n/a	n/a
42	IRF1	chr1:197169275-197169884	K562	blood:	n/a	n/a
43	MAX	chr1:197169783-197170971	MCF-7	breast:	n/a	n/a
44	JUND	chr1:197169146-197171283	K562	blood:	n/a	chr1:197170670-197170684
45	ZNF263	chr1:197169185-197171657	HEK293-T-REx	kidney:	n/a	n/a
46	GATA2	chr1:197169385-197171577	SH-SY5Y	brain:	n/a	chr1:197171049-197171059
47	POLR2A	chr1:197169754-197170952	SK-N-SH	brain:	n/a	n/a
48	ELF1	chr1:197169653-197171043	MCF-7	breast:	n/a	chr1:197170426-197170439 chr1:197170428-197170437 chr1:197170495-197170507 chr1:197170071-197170083 chr1:197170427-197170438 chr1:197170427-197170438
49	POLR2A	chr1:197169744-197171021	Hela-S3	cervix:	n/a	n/a
50	MYC	chr1:197169418-197171047	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:197169410..197171188-chr1:197190699..197192659,2	MCF-7	breast:
2	chr1:197112577..197117711-chr1:197168565..197172597,7	K562	blood:
3	chr1:197112577..197117470-chr1:197168821..197172597,7	K562	blood:

Variant related genes	Relation type
CRB1	TF binding region
ZBTB41	TF binding region
ENSG00000066279	Chromatin interaction
ENSG00000237861	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1034162	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10429911	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10494748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10494749	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10494750	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10494751	0.84[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10732295	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10732296	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10801594	1.00[CHB][hapmap]
rs11800461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11803081	1.00[AMR][1000 genomes]
rs11808524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11808883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11809963	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11810041	0.85[AMR][1000 genomes]
rs11811295	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11811814	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1337165	1.00[AMR][1000 genomes]
rs1412631	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1415217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1556763	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1571964	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16841212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841214	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841219	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841220	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841270	1.00[AMR][1000 genomes]
rs1759013	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1794003	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4915378	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs59820773	1.00[ASN][1000 genomes]
rs61170532	1.00[AMR][1000 genomes]
rs61172533	1.00[ASN][1000 genomes]
rs6677082	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6700604	1.00[ASN][1000 genomes]
rs6702338	1.00[ASN][1000 genomes]
rs6702739	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6703400	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7520503	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7534439	1.00[JPT][hapmap]
rs7535048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	26 gene(s)	inside rSNPs	diseases
2	nsv873071	chr1:197079671-197187605	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv873072	chr1:197079671-197221248	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv873073	chr1:197107074-197221248	Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 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	chr1:197116600-197169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:197159400-197169800	Weak transcription	Lung	lung
3	chr1:197159600-197169800	Weak transcription	Spleen	Spleen
4	chr1:197166200-197170000	Flanking Active TSS	Dnd41	blood
5	chr1:197166400-197171400	Active TSS	K562	blood
6	chr1:197166400-197171600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:197166400-197171600	Active TSS	Right Atrium	heart
8	chr1:197166600-197171600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:197166800-197169800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:197166800-197171400	Active TSS	HSMMtube	muscle
11	chr1:197166800-197171600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:197166800-197171800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:197167200-197171600	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr1:197167200-197171600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:197167200-197171600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:197167200-197171600	Active TSS	Fetal Intestine Large	intestine
17	chr1:197167400-197169800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr1:197167400-197171600	Active TSS	Fetal Muscle Leg	muscle
19	chr1:197167400-197171800	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:197167600-197171600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:197168000-197171600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:197168200-197170000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr1:197168400-197170000	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr1:197168400-197170000	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr1:197168400-197171400	Active TSS	HSMM	muscle
26	chr1:197168400-197171600	Active TSS	Aorta	Aorta
27	chr1:197168400-197171600	Active TSS	Left Ventricle	heart
28	chr1:197168400-197171600	Active TSS	Ovary	ovary
29	chr1:197168400-197171600	Active TSS	Psoas Muscle	Psoas
30	chr1:197168400-197171600	Active TSS	Right Ventricle	heart
31	chr1:197168600-197169800	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr1:197168600-197169800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr1:197168600-197170000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr1:197168600-197171200	Active TSS	Thymus	Thymus
35	chr1:197168600-197171800	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr1:197168800-197171400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:197168800-197171400	Active TSS	Brain Substantia Nigra	brain
38	chr1:197168800-197171800	Active TSS	Stomach Smooth Muscle	stomach
39	chr1:197168800-197172000	Active TSS	NHDF-Ad	bronchial
40	chr1:197169000-197170000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr1:197169000-197170000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr1:197169200-197169800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr1:197169200-197169800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr1:197169200-197169800	Flanking Active TSS	Liver	Liver
45	chr1:197169200-197169800	Flanking Active TSS	Fetal Thymus	thymus
46	chr1:197169200-197169800	Flanking Active TSS	NH-A	brain
47	chr1:197169200-197170000	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr1:197169200-197170000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:197169200-197170000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:197169200-197171200	Active TSS	Fetal Stomach	stomach

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