Variant report

Variant	rs36228834
Chromosome Location	chr9:21975319-21975320
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	MAX	chr9:21974444-21975416	ECC-1	luminal epithelium:	n/a	chr9:21974880-21974887
2	POLR2A	chr9:21974328-21975448	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr9:21974334-21976151	Hela-S3	cervix:	n/a	n/a
4	CTBP2	chr9:21973995-21975634	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr9:21974433-21975662	ECC-1	luminal epithelium:	n/a	n/a
6	SMC3	chr9:21974297-21975824	Hela-S3	cervix:	n/a	chr9:21974893-21974907
7	MAX	chr9:21974498-21975615	ECC-1	luminal epithelium:	n/a	chr9:21974880-21974887
8	GABPA	chr9:21974671-21975425	HL-60	blood:	n/a	chr9:21975224-21975233
9	ZNF143	chr9:21974625-21975484	Hela-S3	cervix:	n/a	chr9:21975184-21975202
10	POLR2A	chr9:21974397-21975455	ECC-1	luminal epithelium:	n/a	n/a
11	EGR1	chr9:21975151-21975357	GM12878	blood:	n/a	chr9:21975277-21975290 chr9:21975278-21975287 chr9:21975277-21975287 chr9:21975277-21975290 chr9:21975276-21975290 chr9:21975276-21975291 chr9:21975223-21975233 chr9:21975277-21975290 chr9:21975274-21975288 chr9:21975277-21975290
12	MAX	chr9:21975294-21975540	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr9:21973555-21975862	Hela-S3	cervix:	n/a	n/a
14	MAX	chr9:21974445-21975381	H1-hESC	embryonic stem cell:	n/a	chr9:21974880-21974887
15	POLR2A	chr9:21973618-21975974	Hela-S3	cervix:	n/a	n/a
16	TAF1	chr9:21974603-21975509	ECC-1	luminal epithelium:	n/a	n/a
17	YY1	chr9:21974558-21975355	ECC-1	luminal epithelium:	n/a	chr9:21975279-21975288 chr9:21974862-21974873 chr9:21975279-21975290
18	REST	chr9:21974644-21975837	HL-60	blood:	n/a	chr9:21975220-21975233
19	MAZ	chr9:21974133-21975785	IMR90	lung:	n/a	chr9:21974880-21974887
20	TCF7L2	chr9:21973903-21975883	Hela-S3	cervix:	n/a	chr9:21975519-21975535 chr9:21975522-21975531 chr9:21975524-21975531 chr9:21975519-21975535
21	JUND	chr9:21974478-21975458	H1-hESC	embryonic stem cell:	n/a	chr9:21975177-21975186
22	MYC	chr9:21974207-21975396	Hela-S3	cervix:	n/a	chr9:21974880-21974887
23	ELF1	chr9:21974628-21975324	GM12878	blood:	n/a	chr9:21975115-21975124
24	MAX	chr9:21974436-21975449	HCT-116	colon:	n/a	chr9:21974880-21974887
25	RCOR1	chr9:21974069-21976007	Hela-S3	cervix:	n/a	n/a
26	NFIC	chr9:21974567-21975603	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr9:21974411-21975453	PFSK-1	brain:	n/a	n/a
28	MXI1	chr9:21974453-21975623	Hela-S3	cervix:	n/a	chr9:21975174-21975183
29	EGR1	chr9:21974669-21975440	H1-hESC	embryonic stem cell:	n/a	chr9:21975277-21975290 chr9:21975278-21975287 chr9:21975277-21975287 chr9:21975277-21975290 chr9:21975276-21975290 chr9:21975276-21975291 chr9:21975223-21975233 chr9:21975277-21975290 chr9:21975274-21975288 chr9:21975277-21975290
30	SUZ12	chr9:21973642-21976348	NT2-D1	testis:	n/a	n/a
31	CHD2	chr9:21974495-21975731	Hela-S3	cervix:	n/a	n/a
32	YY1	chr9:21974453-21975381	H1-hESC	embryonic stem cell:	n/a	chr9:21975279-21975288 chr9:21974862-21974873 chr9:21975279-21975290
33	BRCA1	chr9:21974679-21975657	Hela-S3	cervix:	n/a	n/a
34	EGR1	chr9:21974458-21975399	H1-hESC	embryonic stem cell:	n/a	chr9:21975277-21975290 chr9:21975278-21975287 chr9:21975277-21975287 chr9:21975277-21975290 chr9:21975276-21975290 chr9:21975276-21975291 chr9:21975223-21975233 chr9:21975277-21975290 chr9:21975274-21975288 chr9:21975277-21975290
35	MAX	chr9:21974388-21975412	H1-hESC	embryonic stem cell:	n/a	chr9:21974880-21974887
36	SIN3AK20	chr9:21975049-21975368	PFSK-1	brain:	n/a	n/a
37	TCF12	chr9:21974525-21975474	ECC-1	luminal epithelium:	n/a	chr9:21975174-21975184
38	MAZ	chr9:21974362-21975734	Hela-S3	cervix:	n/a	chr9:21974880-21974887
39	EGR1	chr9:21975011-21975529	ECC-1	luminal epithelium:	n/a	chr9:21975277-21975290 chr9:21975491-21975501 chr9:21975278-21975287 chr9:21975277-21975287 chr9:21975277-21975290 chr9:21975276-21975290 chr9:21975276-21975291 chr9:21975223-21975233 chr9:21975277-21975290 chr9:21975274-21975288 chr9:21975277-21975290
40	GABPA	chr9:21974735-21975319	HL-60	blood:	n/a	chr9:21975224-21975233
41	MXI1	chr9:21974143-21975643	SK-N-SH	brain:	n/a	chr9:21975174-21975183
42	POLR2A	chr9:21974465-21975406	IMR90	lung:	n/a	n/a
43	YY1	chr9:21974557-21975401	ECC-1	luminal epithelium:	n/a	chr9:21975279-21975288 chr9:21974862-21974873 chr9:21975279-21975290
44	TAF1	chr9:21974704-21975433	PFSK-1	brain:	n/a	n/a
45	EGR1	chr9:21974822-21975586	HCT-116	colon:	n/a	chr9:21975277-21975290 chr9:21975491-21975501 chr9:21975278-21975287 chr9:21975277-21975287 chr9:21975277-21975290 chr9:21975276-21975290 chr9:21975276-21975291 chr9:21975223-21975233 chr9:21975277-21975290 chr9:21975274-21975288 chr9:21975277-21975290
46	ZNF263	chr9:21974195-21975984	HEK293-T-REx	kidney:	n/a	chr9:21975166-21975175 chr9:21975151-21975160
47	POLR2A	chr9:21974047-21975863	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr9:21974397-21975793	HL-60	blood:	n/a	n/a
49	POLR2A	chr9:21974238-21975855	SK-N-MC	brain:	n/a	n/a
50	TBP	chr9:21974876-21975837	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
CDKN2A	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs36229158	1.00[AMR][1000 genomes]
rs3731249	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21972600-21975600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr9:21973200-21975600	Active TSS	Hela-S3	cervix
3	chr9:21973200-21976000	Active TSS	HSMMtube	muscle
4	chr9:21973400-21975400	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
5	chr9:21973400-21975400	Bivalent/Poised TSS	NHEK	skin
6	chr9:21973400-21975600	Bivalent/Poised TSS	NH-A	brain
7	chr9:21973400-21979800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:21973600-21975400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:21973600-21975600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr9:21973600-21976000	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
11	chr9:21973800-21975600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:21973800-21976000	Bivalent/Poised TSS	NHLF	lung
13	chr9:21973800-21976200	Active TSS	HSMM	muscle
14	chr9:21973800-21976800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr9:21974000-21975800	Active TSS	Dnd41	blood
16	chr9:21974200-21975400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:21974200-21975400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr9:21974200-21975400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:21974200-21975600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
20	chr9:21974200-21975800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:21974200-21975800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
22	chr9:21974200-21975800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
23	chr9:21974200-21975800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
24	chr9:21974200-21976000	Flanking Bivalent TSS/Enh	Osteobl	bone
25	chr9:21974200-21976200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:21974400-21975400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:21974400-21975400	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
28	chr9:21974400-21975400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
29	chr9:21974400-21975600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:21974400-21975600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
31	chr9:21974400-21975600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
32	chr9:21974400-21975600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:21974400-21975600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
34	chr9:21974400-21975600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:21974400-21975600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:21974400-21975600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
37	chr9:21974400-21975600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
38	chr9:21974400-21975600	Bivalent Enhancer	Fetal Lung	lung
39	chr9:21974400-21975600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
40	chr9:21974400-21975600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
41	chr9:21974400-21975600	Enhancers	Spleen	Spleen
42	chr9:21974400-21975600	Active TSS	GM12878-XiMat	blood
43	chr9:21974400-21975600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
44	chr9:21974400-21975800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr9:21974400-21975800	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
46	chr9:21974400-21975800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
47	chr9:21974400-21975800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
48	chr9:21974400-21975800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
49	chr9:21974400-21975800	Bivalent Enhancer	Fetal Heart	heart
50	chr9:21974400-21976000	Bivalent/Poised TSS	NHDF-Ad	bronchial

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