Variant report

Variant	rs549849109
Chromosome Location	chr9:96716551-96716552
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr9:96709708-96717433	H1-hESC	embryonic stem cell:	n/a	n/a
2	GABPA	chr9:96716515-96716984	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr9:96716169-96718368	Hela-S3	cervix:	n/a	n/a
4	MAX	chr9:96716327-96717225	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr9:96715218-96716678	H1-neurons	neurons:	n/a	n/a
6	E2F6	chr9:96716184-96717258	H1-hESC	embryonic stem cell:	n/a	chr9:96717156-96717171 chr9:96716525-96716533 chr9:96716525-96716533 chr9:96716808-96716818 chr9:96717160-96717172 chr9:96716526-96716533 chr9:96716848-96716858 chr9:96716519-96716529 chr9:96716524-96716534
7	MAX	chr9:96716412-96717217	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTBP2	chr9:96710652-96717425	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	chr9:96716527-96716577	U87	brain:	n/a
2	chr9:96716527-96716577	HPAEpiC	pulmonary alveolar:	n/a
3	chr9:96716527-96716577	GM12892	blood:	n/a
4	chr9:96716527-96716577	HUVEC	blood vessel:	n/a
5	chr9:96716527-96716577	NHDF-neo	bronchial:	n/a
6	chr9:96716527-96716577	NB4	blood:	n/a
7	chr9:96716527-96716577	SK-N-SH	brain:	n/a
8	chr9:96716527-96716577	HNPCEpiC	eye:	n/a
9	chr9:96716527-96716577	RPTEC	kidney:	n/a
10	chr9:96716527-96716577	IMR90	lung:	fetal
11	chr9:96716527-96716577	HCT-116	colon:	n/a
12	chr9:96716527-96716577	Jurkat	blood:	n/a
13	chr9:96716527-96716577	H1-hESC	embryonic stem cell:	embryo
14	chr9:96716527-96716577	HCM	heart:	n/a
15	chr9:96716527-96716577	HMEC	breast:	n/a
16	chr9:96716527-96716577	AG09309	skin:	n/a
17	chr9:96716527-96716577	HEK293	kidney:	embryo
18	chr9:96716527-96716577	SAEC	small airway:	n/a
19	chr9:96716527-96716577	ovcar-3	ovarian:	n/a
20	chr9:96716527-96716577	ProgFib	skin:	n/a
21	chr9:96716527-96716577	HIPEpiC	eye:	n/a
22	chr9:96716527-96716577	K562	blood:	n/a
23	chr9:96716527-96716577	HEEpiC	esophagus:	n/a
24	chr9:96716527-96716577	AG10803	skin:	n/a
25	chr9:96716527-96716577	Caco-2	colon:	n/a
26	chr9:96716527-96716577	MCF-7	breast:	n/a
27	chr9:96716527-96716577	Hepatocyte	liver:	n/a
28	chr9:96716527-96716577	PFSK-1	brain:	n/a
29	chr9:96716527-96716577	GM19239	blood:	n/a
30	chr9:96716527-96716577	AG09319	gingival:	n/a
31	chr9:96716527-96716577	HRE	kidney:	n/a
32	chr9:96716527-96716577	ECC-1	luminal epithelium:	n/a
33	chr9:96716527-96716577	A549	lung:	n/a
34	chr9:96716527-96716577	NHBE	bronchial:	n/a
35	chr9:96716527-96716577	HCPEpiC	choroid plexus:	n/a
36	chr9:96716527-96716577	HCF	heart:	n/a
37	chr9:96716527-96716577	AG04450	lung:	fetal
38	chr9:96716527-96716577	T-47D	breast:	n/a
39	chr9:96716527-96716577	BJ	skin:	n/a
40	chr9:96716527-96716577	HL-60	blood:	n/a
41	chr9:96716527-96716577	SKMC	muscle:	n/a
42	chr9:96716527-96716577	BE2_C	brain:	n/a
43	chr9:96716527-96716577	PANC-1	pancreas:	n/a
44	chr9:96716527-96716577	HepG2	liver:	n/a
45	chr9:96716527-96716577	SK-N-SH_RA	brain:	n/a
46	chr9:96716527-96716577	Hela-S3	cervix:	n/a
47	chr9:96716527-96716577	AG04449	skin:	fetal
48	chr9:96716527-96716577	GM12878	blood:	n/a
49	chr9:96716527-96716577	GM06990	blood:	n/a
50	chr9:96716527-96716577	SK-N-MC	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96709646..96715968-chr9:96715980..96721050,10	MCF-7	breast:

No data

Variant related genes	Relation type
BARX1	TF binding region
ENSG00000235601	TF binding region
ENSG00000235601	CpG island
BARX1	CpG island
ENSG00000131668	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised 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
2	nsv824993	chr9:96699362-96725105	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893590	chr9:96701287-96729129	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3442102	chr9:96716156-96718704	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96713000-96717000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
2	chr9:96713800-96716600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
3	chr9:96713800-96716800	Bivalent Enhancer	Brain Germinal Matrix	brain
4	chr9:96713800-96716800	Bivalent Enhancer	Brain Substantia Nigra	brain
5	chr9:96713800-96717000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr9:96713800-96717200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:96713800-96717400	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr9:96713800-96717800	Bivalent Enhancer	Liver	Liver
9	chr9:96713800-96718400	Bivalent Enhancer	Lung	lung
10	chr9:96714200-96716600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:96714200-96717200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
12	chr9:96714200-96717400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr9:96714200-96717800	Enhancers	Pancreas	Pancrea
14	chr9:96714400-96717000	Bivalent Enhancer	Adipose Nuclei	Adipose
15	chr9:96714400-96717200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr9:96714600-96716800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:96714600-96716800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
18	chr9:96714600-96717000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
19	chr9:96714600-96717000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:96714600-96717000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:96714800-96716800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
22	chr9:96715000-96717000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
23	chr9:96715000-96718800	Bivalent Enhancer	Spleen	Spleen
24	chr9:96715400-96716600	Bivalent Enhancer	Colonic Mucosa	Colon
25	chr9:96715400-96716800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
26	chr9:96715400-96717200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
27	chr9:96715800-96716600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr9:96715800-96717000	Bivalent Enhancer	Brain Hippocampus Middle	brain
29	chr9:96715800-96717000	Weak transcription	Right Atrium	heart
30	chr9:96715800-96717200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr9:96715800-96717200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:96716000-96716600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr9:96716000-96716600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:96716000-96717000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:96716000-96717000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
36	chr9:96716000-96717200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
37	chr9:96716000-96717400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
38	chr9:96716200-96716600	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:96716200-96716600	Flanking Active TSS	Gastric	stomach
40	chr9:96716200-96718200	Active TSS	Osteobl	bone
41	chr9:96716400-96716600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
42	chr9:96716400-96716600	Bivalent/Poised TSS	Primary B cells from cord blood	blood
43	chr9:96716400-96716600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:96716400-96716600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr9:96716400-96716800	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
46	chr9:96716400-96716800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
47	chr9:96716400-96716800	Bivalent Enhancer	Fetal Brain Female	brain
48	chr9:96716400-96717000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
49	chr9:96716400-96717000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
50	chr9:96716400-96717000	Bivalent Enhancer	Placenta	Placenta

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