Variant report

Variant	rs373755298
Chromosome Location	chr6:33409498-33409499
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33408338-33409761	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:33409448-33409498	SK-N-SH	brain:	n/a
2	chr6:33409448-33409498	HCPEpiC	choroid plexus:	n/a
3	chr6:33409448-33409498	GM12891	blood:	n/a
4	chr6:33409448-33409498	HEK293	kidney:	embryo
5	chr6:33409448-33409498	CMK	blood:	n/a
6	chr6:33409448-33409498	U87	brain:	n/a
7	chr6:33409448-33409498	T-47D	breast:	n/a
8	chr6:33409448-33409498	HIPEpiC	eye:	n/a
9	chr6:33409448-33409498	SK-N-MC	brain:	n/a
10	chr6:33409448-33409498	H1-hESC	embryonic stem cell:	embryo
11	chr6:33409448-33409498	HepG2	liver:	n/a
12	chr6:33409448-33409498	A549	lung:	n/a
13	chr6:33409448-33409498	AG09309	skin:	n/a
14	chr6:33409448-33409498	HCF	heart:	n/a
15	chr6:33409448-33409498	HRCEpiC	kidney:	n/a
16	chr6:33409448-33409498	SAEC	small airway:	n/a
17	chr6:33409448-33409498	HRE	kidney:	n/a
18	chr6:33409448-33409498	Caco-2	colon:	n/a
19	chr6:33409448-33409498	AoSMC	blood vessel:	n/a
20	chr6:33409448-33409498	HAEpiC	amniotic membrane:	n/a
21	chr6:33409448-33409498	HEEpiC	esophagus:	n/a
22	chr6:33409448-33409498	HCT-116	colon:	n/a
23	chr6:33409448-33409498	HCM	heart:	n/a
24	chr6:33409448-33409498	GM06990	blood:	n/a
25	chr6:33409448-33409498	LNCaP	prostate:	n/a
26	chr6:33409448-33409498	BJ	skin:	n/a
27	chr6:33409448-33409498	RPTEC	kidney:	n/a
28	chr6:33409448-33409498	K562	blood:	n/a
29	chr6:33409448-33409498	SKMC	muscle:	n/a
30	chr6:33409448-33409498	HL-60	blood:	n/a
31	chr6:33409448-33409498	IMR90	lung:	fetal
32	chr6:33409448-33409498	AG04449	skin:	fetal
33	chr6:33409448-33409498	HPAEpiC	pulmonary alveolar:	n/a
34	chr6:33409448-33409498	GM19239	blood:	n/a
35	chr6:33409448-33409498	GM12878	blood:	n/a
36	chr6:33409448-33409498	AG10803	skin:	n/a
37	chr6:33409448-33409498	AG09319	gingival:	n/a
38	chr6:33409448-33409498	Hela-S3	cervix:	n/a
39	chr6:33409448-33409498	NT2-D1	testis:	n/a
40	chr6:33409448-33409498	NH-A	brain:	n/a
41	chr6:33409448-33409498	AG04450	lung:	fetal
42	chr6:33409448-33409498	GM12892	blood:	n/a
43	chr6:33409448-33409498	BE2_C	brain:	n/a
44	chr6:33409448-33409498	ovcar-3	ovarian:	n/a
45	chr6:33409448-33409498	ProgFib	skin:	n/a
46	chr6:33409448-33409498	HUVEC	blood vessel:	n/a
47	chr6:33409448-33409498	NHBE	bronchial:	n/a
48	chr6:33409448-33409498	Hepatocyte	liver:	n/a
49	chr6:33409448-33409498	NB4	blood:	n/a
50	chr6:33409448-33409498	SK-N-SH_RA	brain:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33404069..33406750-chr6:33407909..33409800,2	MCF-7	breast:
2	chr6:33242343..33245009-chr6:33406887..33409853,3	K562	blood:
3	chr6:33406190..33414491-chr6:33419287..33424467,10	MCF-7	breast:
4	chr6:33399707..33401893-chr6:33408144..33410005,2	MCF-7	breast:

No data

Variant related genes	Relation type
SYNGAP1	TF binding region
SYNGAP1	CpG island
ENSG00000213588	Chromatin interaction
ENSG00000264085	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000197283	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	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
6	nsv437503	chr6:33408542-33421577	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33396600-33416000	Weak transcription	Pancreas	Pancrea
2	chr6:33399400-33421200	Weak transcription	HMEC	breast
3	chr6:33399400-33421600	Weak transcription	Stomach Mucosa	stomach
4	chr6:33399600-33421400	Weak transcription	HUVEC	blood vessel
5	chr6:33399800-33421400	Weak transcription	A549	lung
6	chr6:33400000-33412800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:33400000-33418000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:33400000-33420600	Strong transcription	Brain Germinal Matrix	brain
9	chr6:33400800-33412800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:33401200-33420800	Strong transcription	Fetal Brain Female	brain
11	chr6:33401400-33417600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr6:33401400-33418800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:33401400-33421400	Weak transcription	Right Atrium	heart
14	chr6:33401600-33416600	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:33402000-33417600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:33402000-33418000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:33402000-33418000	Strong transcription	NHLF	lung
18	chr6:33402000-33418200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:33402000-33420600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:33402200-33417400	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr6:33402200-33417400	Strong transcription	Thymus	Thymus
22	chr6:33402200-33418200	Strong transcription	Fetal Muscle Leg	muscle
23	chr6:33402200-33418600	Strong transcription	Dnd41	blood
24	chr6:33402200-33420000	Strong transcription	Fetal Thymus	thymus
25	chr6:33402200-33420800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:33402400-33420800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:33402600-33417600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr6:33402600-33420000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:33402600-33420400	Strong transcription	Fetal Stomach	stomach
30	chr6:33402600-33421400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:33402800-33411000	Strong transcription	Brain Hippocampus Middle	brain
32	chr6:33402800-33417200	Strong transcription	Fetal Intestine Small	intestine
33	chr6:33402800-33417400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:33402800-33417600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:33402800-33417600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:33402800-33417600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:33402800-33417800	Strong transcription	Primary T cells from cord blood	blood
38	chr6:33402800-33417800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:33402800-33418400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:33402800-33418600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr6:33402800-33418600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr6:33402800-33419000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:33402800-33420000	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr6:33402800-33420000	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr6:33402800-33420000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr6:33402800-33420200	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr6:33402800-33420200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr6:33403000-33409800	Strong transcription	Placenta	Placenta
49	chr6:33403000-33410800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:33403000-33411800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links