Variant report

Variant	rs145372890
Chromosome Location	chr6:33399165-33399166
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	ELF1	chr6:33398770-33400290	GM12878	blood:	n/a	chr6:33398973-33398985 chr6:33398859-33398872
2	ZNF143	chr6:33398801-33399439	H1-hESC	embryonic stem cell:	n/a	n/a
3	SIN3A	chr6:33398695-33399700	H1-hESC	embryonic stem cell:	n/a	chr6:33398933-33398942 chr6:33398970-33398981
4	POLR2A	chr6:33398873-33399730	H1-hESC	embryonic stem cell:	n/a	n/a
5	SP1	chr6:33398651-33399516	H1-hESC	embryonic stem cell:	n/a	chr6:33398918-33398930 chr6:33399260-33399274 chr6:33398874-33398888 chr6:33398918-33398930 chr6:33398919-33398928 chr6:33398919-33398933 chr6:33399323-33399337 chr6:33399261-33399270 chr6:33398919-33398928 chr6:33398920-33398929 chr6:33398936-33398957 chr6:33399161-33399175
6	SP1	chr6:33398621-33399599	H1-hESC	embryonic stem cell:	n/a	chr6:33398918-33398930 chr6:33399260-33399274 chr6:33398874-33398888 chr6:33398918-33398930 chr6:33398919-33398928 chr6:33398919-33398933 chr6:33399323-33399337 chr6:33399261-33399270 chr6:33398919-33398928 chr6:33398920-33398929 chr6:33398936-33398957 chr6:33399161-33399175
7	HDAC2	chr6:33399073-33399500	H1-hESC	embryonic stem cell:	n/a	chr6:33399249-33399263
8	CREB1	chr6:33398708-33399510	H1-hESC	embryonic stem cell:	n/a	n/a
9	YY1	chr6:33398663-33399316	GM12878	blood:	n/a	chr6:33398973-33398987 chr6:33398996-33399008
10	BACH1	chr6:33399055-33399426	H1-hESC	embryonic stem cell:	n/a	n/a
11	MXI1	chr6:33398550-33399322	GM12878	blood:	n/a	chr6:33398901-33398916
12	TBP	chr6:33398826-33399553	H1-hESC	embryonic stem cell:	n/a	n/a
13	SP4	chr6:33398865-33399269	H1-hESC	embryonic stem cell:	n/a	chr6:33398916-33398932
14	TEAD4	chr6:33398784-33399487	H1-hESC	embryonic stem cell:	n/a	n/a
15	EP300	chr6:33398671-33399482	H1-hESC	embryonic stem cell:	n/a	chr6:33398920-33398936
16	MAX	chr6:33398751-33399689	H1-hESC	embryonic stem cell:	n/a	chr6:33399285-33399295 chr6:33399302-33399309 chr6:33399420-33399430 chr6:33399300-33399311
17	EP300	chr6:33398975-33399416	H1-hESC	embryonic stem cell:	n/a	n/a
18	GABPA	chr6:33398730-33399234	K562	blood:	n/a	n/a
19	MAX	chr6:33398720-33399447	H1-hESC	embryonic stem cell:	n/a	chr6:33399285-33399295 chr6:33399302-33399309 chr6:33399420-33399430 chr6:33399300-33399311
20	MXI1	chr6:33398710-33399455	H1-hESC	embryonic stem cell:	n/a	chr6:33398901-33398916 chr6:33399333-33399342
21	SIN3AK20	chr6:33398646-33399531	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr6:33398042-33399915	SK-N-MC	brain:	n/a	n/a
23	MAX	chr6:33398789-33399659	H1-hESC	embryonic stem cell:	n/a	chr6:33399285-33399295 chr6:33399302-33399309 chr6:33399420-33399430 chr6:33399300-33399311
24	MYC	chr6:33398775-33399348	NB4	blood:	n/a	chr6:33399285-33399295 chr6:33399302-33399309 chr6:33399300-33399311
25	RELA	chr6:33397963-33399236	GM19099	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
26	TEAD4	chr6:33398820-33399529	H1-hESC	embryonic stem cell:	n/a	n/a
27	BHLHE40	chr6:33398786-33399349	GM12878	blood:	n/a	n/a
28	YY1	chr6:33398747-33399222	GM12892	blood:	n/a	chr6:33398973-33398987 chr6:33398996-33399008
29	MYC	chr6:33399124-33399202	GM12878	blood:	n/a	n/a
30	USF2	chr6:33398898-33399429	H1-hESC	embryonic stem cell:	n/a	n/a
31	CHD2	chr6:33398656-33399325	GM12878	blood:	n/a	chr6:33399261-33399271
32	MAZ	chr6:33398235-33399507	IMR90	lung:	n/a	chr6:33399285-33399295 chr6:33399302-33399309 chr6:33399420-33399430 chr6:33399300-33399311
33	ELF1	chr6:33398562-33399232	MCF-7	breast:	n/a	chr6:33398973-33398985 chr6:33398859-33398872
34	POLR2A	chr6:33398851-33399221	Raji	blood:	n/a	n/a
35	RCOR1	chr6:33398792-33399177	K562	blood:	n/a	n/a
36	MAX	chr6:33399130-33399387	K562	blood:	n/a	chr6:33399285-33399295 chr6:33399302-33399309 chr6:33399300-33399311
37	CEBPB	chr6:33398987-33399359	H1-hESC	embryonic stem cell:	n/a	n/a
38	ATF2	chr6:33398954-33399529	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr6:33398779-33399494	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAX	chr6:33399122-33399434	K562	blood:	n/a	chr6:33399285-33399295 chr6:33399302-33399309 chr6:33399420-33399430 chr6:33399300-33399311
41	MYC	chr6:33399018-33399827	H1-hESC	embryonic stem cell:	n/a	chr6:33399285-33399295 chr6:33399302-33399309 chr6:33399420-33399430 chr6:33399300-33399311
42	SIN3AK20	chr6:33398655-33399230	PFSK-1	brain:	n/a	n/a
43	CHD2	chr6:33398791-33399488	H1-hESC	embryonic stem cell:	n/a	chr6:33399261-33399271
44	YY1	chr6:33398665-33399363	H1-hESC	embryonic stem cell:	n/a	chr6:33398973-33398987 chr6:33398996-33399008
45	SIN3AK20	chr6:33399101-33399418	H1-hESC	embryonic stem cell:	n/a	n/a
46	ELF1	chr6:33398557-33399227	K562	blood:	n/a	chr6:33398973-33398985 chr6:33398859-33398872
47	ATF2	chr6:33398645-33399545	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTBP2	chr6:33398682-33399452	H1-hESC	embryonic stem cell:	n/a	n/a
49	JUND	chr6:33398680-33399383	H1-hESC	embryonic stem cell:	n/a	chr6:33398938-33398947
50	POLR2A	chr6:33398547-33399564	PFSK-1	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:33399151-33399201	K562	blood:	n/a
2	chr6:33399151-33399201	SK-N-SH	brain:	n/a
3	chr6:33399151-33399201	Hepatocyte	liver:	n/a
4	chr6:33399151-33399201	HPAEpiC	pulmonary alveolar:	n/a
5	chr6:33399151-33399201	GM19239	blood:	n/a
6	chr6:33399151-33399201	HEK293	kidney:	embryo
7	chr6:33399151-33399201	AG10803	skin:	n/a
8	chr6:33399151-33399201	HRPEpiC	eye:	n/a
9	chr6:33399151-33399201	IMR90	lung:	fetal
10	chr6:33399151-33399201	U87	brain:	n/a
11	chr6:33399151-33399201	RPTEC	kidney:	n/a
12	chr6:33399151-33399201	HRE	kidney:	n/a
13	chr6:33399151-33399201	AG09319	gingival:	n/a
14	chr6:33399151-33399201	GM06990	blood:	n/a
15	chr6:33399151-33399201	T-47D	breast:	n/a
16	chr6:33399151-33399201	NHBE	bronchial:	n/a
17	chr6:33399151-33399201	MCF-7	breast:	n/a
18	chr6:33399151-33399201	SK-N-MC	brain:	n/a
19	chr6:33399151-33399201	AG09309	skin:	n/a
20	chr6:33399151-33399201	BE2_C	brain:	n/a
21	chr6:33399151-33399201	HCT-116	colon:	n/a
22	chr6:33399151-33399201	LNCaP	prostate:	n/a
23	chr6:33399151-33399201	HAEpiC	amniotic membrane:	n/a
24	chr6:33399151-33399201	HIPEpiC	eye:	n/a
25	chr6:33399151-33399201	NH-A	brain:	n/a
26	chr6:33399151-33399201	CMK	blood:	n/a
27	chr6:33399151-33399201	Caco-2	colon:	n/a
28	chr6:33399151-33399201	PANC-1	pancreas:	n/a
29	chr6:33399151-33399201	PrEC	prostate:	n/a
30	chr6:33399151-33399201	GM12891	blood:	n/a
31	chr6:33399151-33399201	Hela-S3	cervix:	n/a
32	chr6:33399151-33399201	H1-hESC	embryonic stem cell:	embryo
33	chr6:33399151-33399201	ovcar-3	ovarian:	n/a
34	chr6:33399151-33399201	AG04449	skin:	fetal
35	chr6:33399151-33399201	MCF10A-Er-Src	breast:	n/a
36	chr6:33399151-33399201	ECC-1	luminal epithelium:	n/a
37	chr6:33399151-33399201	HCF	heart:	n/a
38	chr6:33399151-33399201	HepG2	liver:	n/a
39	chr6:33399151-33399201	HEEpiC	esophagus:	n/a
40	chr6:33399151-33399201	BJ	skin:	n/a
41	chr6:33399151-33399201	Jurkat	blood:	n/a
42	chr6:33399151-33399201	AoSMC	blood vessel:	n/a
43	chr6:33399151-33399201	HMEC	breast:	n/a
44	chr6:33399151-33399201	HL-60	blood:	n/a
45	chr6:33399151-33399201	SK-N-SH_RA	brain:	n/a
46	chr6:33399151-33399201	NHDF-neo	bronchial:	n/a
47	chr6:33399151-33399201	HNPCEpiC	eye:	n/a
48	chr6:33399151-33399201	HRCEpiC	kidney:	n/a
49	chr6:33399151-33399201	GM12878	blood:	n/a
50	chr6:33399151-33399201	AG04450	lung:	fetal

No.	Distal block	Cell Line	Cell type
1	chr6:33263619..33269524-chr6:33392449..33400505,13	K562	blood:
2	chr6:33395899..33401993-chr6:33420102..33423796,11	MCF-7	breast:
3	chr6:33174005..33176257-chr6:33398590..33400783,2	MCF-7	breast:
4	chr6:33358270..33361160-chr6:33397889..33401606,4	K562	blood:
5	chr6:33398677..33403495-chr6:33419995..33423723,6	K562	blood:
6	chr6:33173944..33176266-chr6:33397713..33400457,2	K562	blood:
7	chr6:33392449..33400629-chr6:33419013..33424035,12	MCF-7	breast:
8	chr6:33237732..33247113-chr6:33390735..33401356,31	K562	blood:
9	chr6:33244147..33247113-chr6:33398461..33400467,3	K562	blood:
10	chr6:33357884..33361160-chr6:33397889..33401606,5	K562	blood:

Variant related genes	Relation type
SYNGAP1	TF binding region
SYNGAP1	CpG island
ENSG00000237649	Chromatin interaction
ENSG00000199036	Chromatin interaction
ENSG00000223501	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000235863	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv885769	chr6:33377522-33412197	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv602832	chr6:33382241-33520221	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats 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 miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv932196	chr6:33383131-33400706	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
6	nsv1019212	chr6:33398031-33413930	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	16 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	chr6:33396000-33401400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:33396200-33399200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:33396200-33399800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
4	chr6:33396200-33400000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr6:33396200-33400000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr6:33396200-33400200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr6:33396200-33400200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr6:33396200-33400400	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr6:33396200-33400400	Flanking Active TSS	GM12878-XiMat	blood
10	chr6:33396400-33399200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:33396400-33401200	Enhancers	Spleen	Spleen
12	chr6:33396400-33401600	Enhancers	Fetal Heart	heart
13	chr6:33396400-33403000	Weak transcription	Ovary	ovary
14	chr6:33396400-33405200	Weak transcription	Psoas Muscle	Psoas
15	chr6:33396600-33399200	Enhancers	Fetal Intestine Small	intestine
16	chr6:33396600-33399200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr6:33396600-33399400	Enhancers	HMEC	breast
18	chr6:33396600-33399600	Enhancers	Liver	Liver
19	chr6:33396600-33399600	Enhancers	Fetal Intestine Large	intestine
20	chr6:33396600-33399600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr6:33396600-33400600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr6:33396600-33400600	Enhancers	Fetal Muscle Leg	muscle
23	chr6:33396600-33400600	Enhancers	Lung	lung
24	chr6:33396600-33400800	Weak transcription	Right Atrium	heart
25	chr6:33396600-33401000	Weak transcription	HSMMtube	muscle
26	chr6:33396600-33416000	Weak transcription	Pancreas	Pancrea
27	chr6:33396800-33399200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:33396800-33399800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:33396800-33402000	Enhancers	Fetal Lung	lung
30	chr6:33396800-33403000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:33396800-33403000	Weak transcription	Aorta	Aorta
32	chr6:33397000-33399400	Enhancers	NHEK	skin
33	chr6:33397200-33399600	Enhancers	HUVEC	blood vessel
34	chr6:33397200-33399800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr6:33397200-33400800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr6:33397600-33400000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:33397800-33399400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:33398000-33399400	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr6:33398000-33399400	Enhancers	Stomach Mucosa	stomach
40	chr6:33398000-33399600	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr6:33398000-33399600	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr6:33398000-33400000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr6:33398000-33400200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr6:33398000-33401400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:33398200-33399200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:33398200-33399200	Enhancers	NHDF-Ad	bronchial
47	chr6:33398200-33399400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr6:33398200-33399400	Enhancers	Esophagus	oesophagus
49	chr6:33398200-33399600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:33398200-33399600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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