Variant report

Variant	rs2811711
Chromosome Location	chr9:21993964-21993965
allele	C/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	chr9:21993452-21995541	GM18505	blood:	n/a	n/a
2	TAF1	chr9:21993776-21994469	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr9:21993892-21996090	GM19193	blood:	n/a	n/a
4	SPI1	chr9:21993454-21994268	HL-60	blood:	n/a	n/a
5	BCLAF1	chr9:21993758-21994467	GM12878	blood:	n/a	n/a
6	GATA2	chr9:21993911-21994294	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr9:21993809-21996161	IMR90	lung:	n/a	n/a
8	POLR2A	chr9:21993354-21995604	GM12892	blood:	n/a	n/a
9	POLR2A	chr9:21992900-21997295	Hela-S3	cervix:	n/a	n/a
10	TAF1	chr9:21993871-21994439	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr9:21993295-21996336	HL-60	blood:	n/a	n/a
12	RAD21	chr9:21993928-21994358	Hela-S3	cervix:	n/a	n/a
13	GATA3	chr9:21993843-21994470	T-47D	breast:	n/a	n/a
14	PML	chr9:21993847-21995741	GM12878	blood:	n/a	n/a
15	POLR2A	chr9:21993952-21996245	GM18951	blood:	n/a	n/a
16	RFX5	chr9:21993205-21996658	Hela-S3	cervix:	n/a	chr9:21995409-21995424 chr9:21995409-21995424 chr9:21995409-21995424
17	ZNF263	chr9:21993295-21994411	HEK293-T-REx	kidney:	n/a	n/a
18	TBP	chr9:21993093-21995427	Hela-S3	cervix:	n/a	n/a
19	MAZ	chr9:21993697-21996161	IMR90	lung:	n/a	n/a
20	POLR2A	chr9:21993831-21994446	GM12892	blood:	n/a	n/a
21	SIN3AK20	chr9:21993758-21994469	PFSK-1	brain:	n/a	n/a
22	RCOR1	chr9:21993506-21996650	Hela-S3	cervix:	n/a	n/a
23	MAZ	chr9:21993538-21996183	Hela-S3	cervix:	n/a	n/a
24	CEBPB	chr9:21993452-21995279	Hela-S3	cervix:	n/a	n/a
25	REST	chr9:21993745-21994541	HL-60	blood:	n/a	n/a
26	MYC	chr9:21993713-21996416	Hela-S3	cervix:	n/a	n/a
27	SUZ12	chr9:21993336-21994460	H1-hESC	embryonic stem cell:	n/a	n/a
28	HA-E2F1	chr9:21993736-21996126	MCF-7	breast:	n/a	chr9:21994670-21994677 chr9:21994669-21994680 chr9:21994669-21994681 chr9:21994670-21994677 chr9:21994651-21994662 chr9:21995794-21995806 chr9:21994670-21994677
29	POLR2A	chr9:21993100-21994516	H1-neurons	neurons:	n/a	n/a
30	MXI1	chr9:21993196-21996229	SK-N-SH	brain:	n/a	chr9:21995410-21995425 chr9:21995408-21995423
31	POLR2A	chr9:21993381-21996933	Hela-S3	cervix:	n/a	n/a
32	ZNF143	chr9:21993697-21995538	Hela-S3	cervix:	n/a	n/a
33	TCF7L2	chr9:21993371-21994433	Hela-S3	cervix:	n/a	n/a
34	MTA3	chr9:21993465-21994476	GM12878	blood:	n/a	n/a
35	MAX	chr9:21993127-21996787	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr9:21993902-21994719	PFSK-1	brain:	n/a	n/a
37	MXI1	chr9:21993480-21996753	Hela-S3	cervix:	n/a	chr9:21995410-21995425 chr9:21995408-21995423
38	POLR2A	chr9:21993526-21995480	GM12878	blood:	n/a	n/a
39	MAX	chr9:21993949-21995639	GM12878	blood:	n/a	n/a
40	POLR2A	chr9:21993360-21995956	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr9:21993363-21995930	Raji	blood:	n/a	n/a
42	POLR2A	chr9:21993846-21994505	GM12878	blood:	n/a	n/a
43	MAX	chr9:21993915-21996081	ECC-1	luminal epithelium:	n/a	n/a
44	RUNX3	chr9:21993827-21994457	GM12878	blood:	n/a	n/a
45	MAX	chr9:21993711-21996662	HCT-116	colon:	n/a	n/a
46	POLR2A	chr9:21993860-21994488	GM12892	blood:	n/a	n/a
47	POLR2A	chr9:21993121-21994496	H1-neurons	neurons:	n/a	n/a
48	TCF7L2	chr9:21993843-21996420	HCT-116	colon:	n/a	n/a
49	CTBP2	chr9:21993378-21994378	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr9:21993342-21996491	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:21801607..21803714-chr9:21992951..21995865,2	MCF-7	breast:
2	chr9:21811532..21820564-chr9:21988281..21997291,17	MCF-7	breast:
3	chr9:21811237..21820561-chr9:21988636..21997115,18	MCF-7	breast:
4	chr9:21992827..21995558-chr9:22007456..22010608,5	MCF-7	breast:
5	chr9:21991860..21994281-chr9:22027750..22030080,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDKN2B-2	chr9:21993881-21994067	NONHSAT130411

Variant related genes	Relation type
CDKN2B-AS1	TF binding region
ENSG00000266446	TF binding region
ENSG00000229298	Chromatin interaction
ENSG00000099810	Chromatin interaction
ENSG00000264545	Chromatin interaction
ENSG00000147883	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13297747	0.81[EUR][1000 genomes]
rs2518719	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs3731198	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3731204	1.00[CEU][hapmap]
rs3731217	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3731222	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs495490	0.85[CEU][hapmap]
rs575427	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv892745	chr9:21857244-22006273	Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv1821117	chr9:21933029-22012229	Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1018514	chr9:21944275-22075326	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv892746	chr9:21953137-22028801	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	esv3492902	chr9:21971026-22006145	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv3492901	chr9:21971095-22006263	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv892747	chr9:21984661-22068646	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21990400-21994000	Weak transcription	Gastric	stomach
2	chr9:21991600-21995800	Active TSS	HMEC	breast
3	chr9:21992000-21996400	Active TSS	Dnd41	blood
4	chr9:21992800-21994200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:21992800-21994200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr9:21992800-21996000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:21992800-21996200	Active TSS	Hela-S3	cervix
8	chr9:21993000-21994200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:21993000-21994200	Flanking Active TSS	NHEK	skin
10	chr9:21993000-21996000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:21993000-21996200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:21993200-21994000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
13	chr9:21993200-21994000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:21993200-21994000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
15	chr9:21993200-21994000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr9:21993200-21994000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
17	chr9:21993200-21994000	Flanking Active TSS	Osteobl	bone
18	chr9:21993200-21995600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr9:21993200-21996400	Active TSS	NHDF-Ad	bronchial
20	chr9:21993400-21994000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:21993400-21994000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:21993400-21994000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
23	chr9:21993400-21994000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:21993400-21994000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
25	chr9:21993400-21994000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
26	chr9:21993400-21994000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:21993400-21994000	Enhancers	Spleen	Spleen
28	chr9:21993400-21994000	Flanking Active TSS	GM12878-XiMat	blood
29	chr9:21993400-21994000	Flanking Active TSS	NH-A	brain
30	chr9:21993400-21994200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
31	chr9:21993400-21994200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
32	chr9:21993400-21994400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
33	chr9:21993400-21994400	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr9:21993400-21994400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
35	chr9:21993400-21994400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:21993400-21996000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:21993400-21996000	Active TSS	HSMMtube	muscle
38	chr9:21993400-21996600	Active TSS	NHLF	lung
39	chr9:21993400-21996800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
40	chr9:21993400-21997000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr9:21993600-21994000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
42	chr9:21993600-21994000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr9:21993600-21994000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
44	chr9:21993600-21994000	Bivalent/Poised TSS	Brain Substantia Nigra	brain
45	chr9:21993600-21994000	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
46	chr9:21993600-21994000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
47	chr9:21993600-21994000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr9:21993600-21994000	Flanking Active TSS	Placenta	Placenta
49	chr9:21993600-21994000	Bivalent Enhancer	Stomach Mucosa	stomach
50	chr9:21993600-21994200	Flanking Active TSS	Primary B cells from peripheral blood	blood

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