Variant report

Variant	rs73656933
Chromosome Location	chr9:102860449-102860450
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	POLR2A	chr9:102860231-102861995	GM12891	blood:	n/a	n/a
2	POLR2A	chr9:102860355-102862257	GM19099	blood:	n/a	n/a
3	RCOR1	chr9:102860278-102862229	K562	blood:	n/a	n/a
4	CREB1	chr9:102860419-102862237	HepG2	liver:	n/a	n/a
5	TAF1	chr9:102860447-102861946	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD2	chr9:102860442-102861750	H1-hESC	embryonic stem cell:	n/a	n/a
7	ELF1	chr9:102860349-102860795	A549	lung:	n/a	n/a
8	POLR2A	chr9:102860319-102862220	GM12878	blood:	n/a	n/a
9	ELF1	chr9:102860335-102860925	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr9:102860405-102862329	GM18505	blood:	n/a	n/a
11	BCLAF1	chr9:102860428-102862100	GM12878	blood:	n/a	chr9:102861317-102861326 chr9:102861219-102861228
12	SIN3AK20	chr9:102860419-102860888	HepG2	liver:	n/a	n/a
13	SREBP1	chr9:102860148-102862462	GM12878	blood:	n/a	n/a
14	SIN3A	chr9:102860305-102862418	H1-hESC	embryonic stem cell:	n/a	n/a
15	MXI1	chr9:102860316-102862307	HepG2	liver:	n/a	n/a
16	RUNX3	chr9:102860375-102862397	GM12878	blood:	n/a	n/a
17	POLR2A	chr9:102860315-102862295	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr9:102860261-102861506	GM12891	blood:	n/a	n/a
19	PML	chr9:102860417-102862048	GM12878	blood:	n/a	n/a
20	CUX1	chr9:102860252-102860693	GM12878	blood:	n/a	n/a
21	POLR2A	chr9:102860233-102861686	K562	blood:	n/a	n/a
22	NFYB	chr9:102860354-102860832	GM12878	blood:	n/a	chr9:102860580-102860595 chr9:102860580-102860595 chr9:102860579-102860591
23	TEAD4	chr9:102860208-102861498	K562	blood:	n/a	n/a
24	POLR2A	chr9:102860405-102862192	K562	blood:	n/a	n/a
25	POLR2A	chr9:102860441-102861905	PBDE	blood:	n/a	n/a
26	NRF1	chr9:102860427-102860681	GM12878	blood:	n/a	n/a
27	SIN3AK20	chr9:102860228-102862468	MCF-7	breast:	n/a	n/a
28	POLR2A	chr9:102860219-102861867	GM12878	blood:	n/a	n/a
29	POLR2A	chr9:102860266-102862328	H1-neurons	neurons:	n/a	n/a
30	POLR2A	chr9:102860445-102862287	GM19193	blood:	n/a	n/a
31	WRNIP1	chr9:102860254-102862321	GM12878	blood:	n/a	n/a
32	MXI1	chr9:102860222-102862815	IMR90	lung:	n/a	n/a
33	NFYA	chr9:102860289-102860775	K562	blood:	n/a	chr9:102860580-102860595 chr9:102860580-102860595 chr9:102860579-102860591
34	ELF1	chr9:102860259-102861870	MCF-7	breast:	n/a	chr9:102861317-102861328 chr9:102861317-102861328 chr9:102861318-102861327
35	SIN3AK20	chr9:102860342-102861568	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr9:102860438-102861948	ECC-1	luminal epithelium:	n/a	n/a
37	POU2F2	chr9:102860280-102861949	GM12878	blood:	n/a	chr9:102860404-102860426 chr9:102860411-102860424 chr9:102860411-102860424 chr9:102860417-102860425 chr9:102860409-102860423 chr9:102860411-102860424 chr9:102860412-102860426
38	HCFC1	chr9:102860073-102862658	Hela-S3	cervix:	n/a	n/a
39	NFYA	chr9:102860356-102861652	Hela-S3	cervix:	n/a	chr9:102860580-102860595 chr9:102860580-102860595 chr9:102860579-102860591
40	POLR2A	chr9:102860397-102860798	HCT-116	colon:	n/a	n/a
41	POLR2A	chr9:102860379-102862267	MCF-7	breast:	n/a	n/a
42	MAX	chr9:102860391-102862442	A549	lung:	n/a	chr9:102861825-102861835
43	RUNX3	chr9:102860401-102862333	GM12878	blood:	n/a	n/a
44	ELF1	chr9:102860341-102860751	HepG2	liver:	n/a	n/a
45	ATF2	chr9:102860343-102860943	GM12878	blood:	n/a	n/a
46	MYBL2	chr9:102860330-102860784	HepG2	liver:	n/a	n/a
47	POLR2A	chr9:102860234-102862265	GM12878	blood:	n/a	n/a
48	POLR2A	chr9:102860418-102862271	Hela-S3	cervix:	n/a	n/a
49	SMARCC2	chr9:102860356-102862282	Hela-S3	cervix:	n/a	chr9:102861352-102861361 chr9:102861513-102861522
50	E2F4	chr9:102860006-102860746	MCF10A-Er-Src	breast:	n/a	chr9:102860582-102860591

No.	Distal block	Cell Line	Cell type
1	chr9:102859693..102862029-chr9:102863024..102865040,3	MCF-7	breast:
2	chr9:102846170..102848209-chr9:102858756..102860662,2	K562	blood:
3	chr9:102860210..102863951-chr9:102865614..102871017,5	K562	blood:
4	chr9:102667836..102670748-chr9:102860445..102862735,2	K562	blood:
5	chr9:102848064..102853071-chr9:102854113..102861263,11	K562	blood:
6	chr9:102581254..102583712-chr9:102860113..102863116,3	K562	blood:

Variant related genes	Relation type
RN7SL75P	TF binding region
INVS	TF binding region
ENSG00000237461	Chromatin interaction
ENSG00000136874	Chromatin interaction
ENSG00000255145	Chromatin interaction
ENSG00000119509	Chromatin interaction
ENSG00000239908	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1338122	1.00[AMR][1000 genomes]
rs1529194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16918894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55773628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55813162	1.00[AMR][1000 genomes]
rs56265710	1.00[AMR][1000 genomes]
rs57518655	1.00[AMR][1000 genomes]
rs59679784	1.00[AMR][1000 genomes]
rs59700543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60045005	1.00[AMR][1000 genomes]
rs61521457	1.00[AMR][1000 genomes]
rs61636243	1.00[AMR][1000 genomes]
rs73655135	1.00[AMR][1000 genomes]
rs73656926	1.00[AMR][1000 genomes]
rs73656927	1.00[AMR][1000 genomes]
rs73656929	1.00[AMR][1000 genomes]
rs73656930	1.00[AMR][1000 genomes]
rs73656932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73656934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73656935	1.00[AMR][1000 genomes]
rs73656937	1.00[AMR][1000 genomes]
rs73656938	1.00[AMR][1000 genomes]
rs73656939	1.00[AMR][1000 genomes]
rs73656949	1.00[AMR][1000 genomes]
rs73656950	1.00[AMR][1000 genomes]
rs73656951	1.00[AMR][1000 genomes]
rs73656954	1.00[AMR][1000 genomes]
rs73656955	1.00[AMR][1000 genomes]
rs73656957	1.00[AMR][1000 genomes]
rs7847283	1.00[AMR][1000 genomes]
rs7848856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7867381	1.00[AMR][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	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1048674	chr9:102752236-103038259	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1052007	chr9:102766948-103033937	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102859200-102862400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:102859200-102862600	Active TSS	GM12878-XiMat	blood
3	chr9:102859200-102862600	Active TSS	K562	blood
4	chr9:102859600-102860600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:102859600-102860600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr9:102859600-102860600	Flanking Active TSS	Dnd41	blood
7	chr9:102859600-102860600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr9:102859600-102860800	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr9:102859600-102861000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:102859600-102862800	Active TSS	NHLF	lung
11	chr9:102859800-102860600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:102859800-102860600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:102859800-102860600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr9:102859800-102860600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:102859800-102860600	Flanking Active TSS	Fetal Heart	heart
16	chr9:102859800-102860600	Flanking Active TSS	HUVEC	blood vessel
17	chr9:102859800-102860800	Flanking Active TSS	Fetal Brain Male	brain
18	chr9:102859800-102862200	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr9:102860000-102860600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:102860000-102860600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:102860000-102860600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr9:102860000-102860600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:102860000-102860600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr9:102860000-102860600	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr9:102860000-102860600	Flanking Active TSS	Hela-S3	cervix
26	chr9:102860000-102860800	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr9:102860000-102860800	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr9:102860000-102860800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr9:102860000-102860800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr9:102860000-102860800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr9:102860000-102860800	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr9:102860000-102860800	Flanking Active TSS	Fetal Brain Female	brain
33	chr9:102860000-102860800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr9:102860000-102860800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr9:102860000-102861000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:102860000-102861000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr9:102860000-102861000	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr9:102860000-102861200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr9:102860000-102862200	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr9:102860000-102862600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:102860000-102862600	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr9:102860000-102862600	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr9:102860000-102862600	Active TSS	NHDF-Ad	bronchial
44	chr9:102860000-102862800	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr9:102860000-102862800	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr9:102860200-102860600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr9:102860200-102860600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr9:102860200-102860600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr9:102860200-102860600	Flanking Active TSS	Liver	Liver
50	chr9:102860200-102860600	Flanking Active TSS	Brain Angular Gyrus	brain

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