Variant report

Variant	rs540298500
Chromosome Location	chr9:6412684-6412685
allele	A/C
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	BCL11A	chr9:6412600-6413034	GM12878	blood:	n/a	n/a
2	MAX	chr9:6412370-6413748	GM12878	blood:	n/a	chr9:6412718-6412727 chr9:6413671-6413681 chr9:6412905-6412915
3	RELA	chr9:6412529-6413464	GM10847	blood:	n/a	n/a
4	RCOR1	chr9:6412425-6413325	K562	blood:	n/a	n/a
5	CHD1	chr9:6412299-6412888	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr9:6412592-6414369	GM12878	blood:	n/a	n/a
7	RELA	chr9:6412442-6413425	GM19099	blood:	n/a	n/a
8	POLR2A	chr9:6412266-6414516	GM12878	blood:	n/a	n/a
9	SP4	chr9:6412481-6413319	H1-hESC	embryonic stem cell:	n/a	chr9:6413038-6413054 chr9:6412902-6412918 chr9:6413040-6413051
10	MAX	chr9:6412417-6413494	HUVEC	blood vessel:	n/a	chr9:6412718-6412727 chr9:6412905-6412915
11	CBX3	chr9:6412407-6413211	K562	blood:	n/a	n/a
12	SETDB1	chr9:6412502-6413013	U2OS	brain:	n/a	n/a
13	TBP	chr9:6412330-6414082	H1-hESC	embryonic stem cell:	n/a	n/a
14	BCLAF1	chr9:6412420-6413716	GM12878	blood:	n/a	chr9:6413655-6413664 chr9:6413653-6413666 chr9:6412547-6412560 chr9:6412552-6412565
15	CHD2	chr9:6412457-6414120	GM12878	blood:	n/a	n/a
16	POU2F2	chr9:6412512-6413329	GM12878	blood:	n/a	n/a
17	STAT1	chr9:6412645-6413546	GM12878	blood:	n/a	n/a
18	POLR2A	chr9:6412447-6413671	HUVEC	blood vessel:	n/a	n/a
19	TCF12	chr9:6412488-6413305	GM12878	blood:	n/a	n/a
20	POLR2A	chr9:6412398-6414036	GM15510	blood:	n/a	n/a
21	BACH1	chr9:6412549-6413272	H1-hESC	embryonic stem cell:	n/a	n/a
22	STAT5A	chr9:6412509-6413260	GM12878	blood:	n/a	n/a
23	POLR2A	chr9:6412615-6414140	Raji	blood:	n/a	n/a
24	TAF1	chr9:6412081-6414376	H1-hESC	embryonic stem cell:	n/a	n/a
25	RELA	chr9:6412436-6413707	GM12892	blood:	n/a	n/a
26	SETDB1	chr9:6412380-6413612	K562	blood:	n/a	n/a
27	POLR2A	chr9:6412214-6414151	HL-60	blood:	n/a	n/a
28	BCLAF1	chr9:6412664-6413695	GM12878	blood:	n/a	chr9:6413655-6413664 chr9:6413653-6413666
29	POLR2A	chr9:6412425-6414240	GM19099	blood:	n/a	n/a
30	CTCF	chr9:6412600-6412750	NHEK	skin:	n/a	n/a
31	POLR2A	chr9:6412563-6412865	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr9:6412176-6414533	GM12892	blood:	n/a	n/a
33	ETS1	chr9:6412511-6413366	GM12878	blood:	n/a	n/a
34	CTBP2	chr9:6412371-6413332	H1-hESC	embryonic stem cell:	n/a	n/a
35	SPI1	chr9:6412400-6413496	HL-60	blood:	n/a	chr9:6413116-6413125 chr9:6413117-6413124
36	POLR2A	chr9:6412572-6413654	GM12891	blood:	n/a	n/a
37	SP1	chr9:6412642-6413735	HCT-116	colon:	n/a	chr9:6413040-6413052 chr9:6412902-6412914 chr9:6413041-6413051 chr9:6413041-6413051 chr9:6413041-6413050 chr9:6413041-6413050 chr9:6412902-6412914 chr9:6413040-6413051 chr9:6413040-6413052 chr9:6413042-6413051
38	PAX5	chr9:6412415-6413480	GM12892	blood:	n/a	n/a
39	MEF2A	chr9:6412485-6413287	GM12878	blood:	n/a	n/a
40	NFATC1	chr9:6412499-6413359	GM12878	blood:	n/a	n/a
41	RXRA	chr9:6412532-6413120	GM12878	blood:	n/a	chr9:6412985-6412992 chr9:6412537-6412544 chr9:6413058-6413065
42	POLR2A	chr9:6412610-6413795	PBDE	blood:	n/a	n/a
43	MXI1	chr9:6412366-6416143	IMR90	lung:	n/a	n/a
44	POLR2A	chr9:6412330-6413698	GM12892	blood:	n/a	n/a
45	EP300	chr9:6412585-6413405	GM12878	blood:	n/a	n/a
46	POLR2A	chr9:6412067-6414007	H1-hESC	embryonic stem cell:	n/a	n/a
47	TBL1XR1	chr9:6412499-6413327	GM12878	blood:	n/a	n/a
48	PML	chr9:6412673-6413345	GM12878	blood:	n/a	n/a
49	MAZ	chr9:6412630-6414011	K562	blood:	n/a	chr9:6412718-6412727 chr9:6413671-6413681 chr9:6412905-6412915
50	E2F6	chr9:6412502-6413382	A549	lung:	n/a	chr9:6412653-6412660 chr9:6412627-6412637 chr9:6412629-6412636 chr9:6412628-6412636 chr9:6412625-6412636 chr9:6412653-6412660 chr9:6412628-6412636 chr9:6412653-6412660 chr9:6412620-6412635 chr9:6412804-6412813 chr9:6412626-6412637 chr9:6412652-6412661 chr9:6412629-6412636 chr9:6412629-6412636

No.	Distal block	Cell Line	Cell type
1	chr1:94312260..94313044-chr9:6412226..6412915,2	NB4	blood:
2	chr9:6410972..6413613-chr9:6564070..6565701,2	MCF-7	breast:
3	chr9:6411580..6414419-chr9:6755713..6757647,2	K562	blood:
4	chr9:6411739..6415458-chr9:6420668..6426596,8	K562	blood:
5	chr2:85132788..85133313-chr9:6412396..6412970,2	NB4	blood:
6	chr15:44718353..44719694-chr9:6411917..6413110,3	NB4	blood:
7	chr9:6412168..6415418-chr9:6418500..6425043,7	MCF-7	breast:
8	chr9:6411889..6413422-chr9:6565833..6568598,2	K562	blood:
9	chr11:64546386..64547209-chr9:6411955..6412774,2	NB4	blood:
10	chr9:6412621..6414719-chr9:6496485..6499094,2	K562	blood:

Variant related genes	Relation type
UHRF2	TF binding region
ENSG00000211575	Chromatin interaction
ENSG00000269038	Chromatin interaction
ENSG00000252110	Chromatin interaction
ENSG00000259595	Chromatin interaction
ENSG00000137770	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000178445	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000107077	Chromatin interaction
ENSG00000147854	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS 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 target site	28 gene(s)	inside rSNPs	diseases
5	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv892160	chr9:6364449-6506038	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv892161	chr9:6364449-6523056	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
12	nsv1023419	chr9:6393886-6415025	Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	esv3440128	chr9:6412477-6415325	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 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	chr9:6411800-6414200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr9:6411800-6414800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr9:6411800-6415200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr9:6411800-6415600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr9:6412000-6414600	Active TSS	Brain Cingulate Gyrus	brain
6	chr9:6412200-6412800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:6412200-6412800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr9:6412200-6412800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr9:6412200-6412800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr9:6412200-6412800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr9:6412200-6412800	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr9:6412200-6412800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr9:6412200-6412800	Flanking Active TSS	Fetal Muscle Leg	muscle
14	chr9:6412200-6412800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
15	chr9:6412200-6413000	Flanking Active TSS	Primary B cells from peripheral blood	blood
16	chr9:6412200-6413000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr9:6412200-6413000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:6412200-6413000	Flanking Active TSS	Fetal Muscle Trunk	muscle
19	chr9:6412200-6413000	Flanking Active TSS	Placenta	Placenta
20	chr9:6412200-6413000	Flanking Active TSS	Fetal Thymus	thymus
21	chr9:6412200-6413000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr9:6412200-6413000	Flanking Active TSS	Thymus	Thymus
23	chr9:6412200-6414200	Active TSS	H1 Cell Line	embryonic stem cell
24	chr9:6412200-6414200	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr9:6412200-6414200	Active TSS	Duodenum Mucosa	Duodenum
26	chr9:6412200-6414400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr9:6412200-6414400	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr9:6412200-6414400	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr9:6412200-6414600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:6412200-6414600	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr9:6412200-6414600	Active TSS	Brain Substantia Nigra	brain
32	chr9:6412200-6414600	Active TSS	Colonic Mucosa	Colon
33	chr9:6412200-6414600	Active TSS	Colon Smooth Muscle	Colon
34	chr9:6412200-6414600	Active TSS	Fetal Heart	heart
35	chr9:6412200-6414600	Active TSS	Fetal Lung	lung
36	chr9:6412200-6414600	Active TSS	Rectal Smooth Muscle	rectum
37	chr9:6412200-6414600	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr9:6412200-6414600	Active TSS	Osteobl	bone
39	chr9:6412200-6414800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:6412200-6414800	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr9:6412200-6414800	Active TSS	Brain Hippocampus Middle	brain
42	chr9:6412200-6414800	Active TSS	Fetal Kidney	kidney
43	chr9:6412200-6414800	Active TSS	Left Ventricle	heart
44	chr9:6412200-6415200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:6412200-6415200	Active TSS	Aorta	Aorta
46	chr9:6412200-6415200	Active TSS	Right Atrium	heart
47	chr9:6412200-6415400	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr9:6412200-6415400	Active TSS	Fetal Intestine Large	intestine
49	chr9:6412200-6415400	Active TSS	Ovary	ovary
50	chr9:6412200-6415400	Active TSS	Psoas Muscle	Psoas

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