Variant report

Variant	rs62119432
Chromosome Location	chr2:9753939-9753940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:9750980-9757087	HepG2	liver:	n/a	n/a
2	CTCF	chr2:9753900-9754050	AoAF	blood vessel:	n/a	n/a
3	CTCF	chr2:9753920-9754070	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:9753409-9754390	PANC-1	pancreas:	n/a	n/a
5	CTCF	chr2:9753920-9754070	HCFaa	heart:	n/a	n/a
6	POLR2A	chr2:9753816-9754270	GM12892	blood:	n/a	n/a
7	KAP1	chr2:9753417-9754135	U2OS	brain:	n/a	n/a
8	CEBPB	chr2:9753405-9754161	IMR90	lung:	n/a	chr2:9753472-9753483 chr2:9753598-9753609
9	POLR2A	chr2:9752087-9755033	A549	lung:	n/a	n/a
10	CTCF	chr2:9753900-9754050	HMF	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:9753939-9753989	NHBE	bronchial:	n/a
2	chr2:9753939-9753989	AG04450	lung:	fetal
3	chr2:9753939-9753989	AG04449	skin:	fetal
4	chr2:9753939-9753989	HMEC	breast:	n/a
5	chr2:9753939-9753989	A549	lung:	n/a
6	chr2:9753939-9753989	Caco-2	colon:	n/a
7	chr2:9753939-9753989	GM12878	blood:	n/a
8	chr2:9753939-9753989	HAEpiC	amniotic membrane:	n/a
9	chr2:9753939-9753989	BE2_C	brain:	n/a
10	chr2:9753939-9753989	ECC-1	luminal epithelium:	n/a
11	chr2:9753939-9753989	NH-A	brain:	n/a
12	chr2:9753939-9753989	U87	brain:	n/a
13	chr2:9753939-9753989	HCPEpiC	choroid plexus:	n/a
14	chr2:9753939-9753989	NT2-D1	testis:	n/a
15	chr2:9753939-9753989	SK-N-MC	brain:	n/a
16	chr2:9753939-9753989	K562	blood:	n/a
17	chr2:9753939-9753989	HepG2	liver:	n/a
18	chr2:9753939-9753989	GM12891	blood:	n/a
19	chr2:9753939-9753989	HRPEpiC	eye:	n/a
20	chr2:9753939-9753989	HNPCEpiC	eye:	n/a
21	chr2:9753939-9753989	SK-N-SH	brain:	n/a
22	chr2:9753939-9753989	Hepatocyte	liver:	n/a
23	chr2:9753939-9753989	HRCEpiC	kidney:	n/a
24	chr2:9753939-9753989	MCF10A-Er-Src	breast:	n/a
25	chr2:9753939-9753989	SAEC	small airway:	n/a
26	chr2:9753939-9753989	RPTEC	kidney:	n/a
27	chr2:9753939-9753989	AG09309	skin:	n/a
28	chr2:9753939-9753989	HEK293	kidney:	embryo
29	chr2:9753939-9753989	HEEpiC	esophagus:	n/a
30	chr2:9753939-9753989	Jurkat	blood:	n/a
31	chr2:9753939-9753989	GM19239	blood:	n/a
32	chr2:9753939-9753989	GM06990	blood:	n/a
33	chr2:9753939-9753989	IMR90	lung:	fetal
34	chr2:9753939-9753989	ovcar-3	ovarian:	n/a
35	chr2:9753939-9753989	PrEC	prostate:	n/a
36	chr2:9753939-9753989	PANC-1	pancreas:	n/a
37	chr2:9753939-9753989	HCT-116	colon:	n/a
38	chr2:9753939-9753989	SKMC	muscle:	n/a
39	chr2:9753939-9753989	HRE	kidney:	n/a
40	chr2:9753939-9753989	SK-N-SH_RA	brain:	n/a
41	chr2:9753939-9753989	LNCaP	prostate:	n/a
42	chr2:9753939-9753989	AG10803	skin:	n/a
43	chr2:9753939-9753989	NHDF-neo	bronchial:	n/a
44	chr2:9753939-9753989	AoSMC	blood vessel:	n/a
45	chr2:9753939-9753989	HCM	heart:	n/a
46	chr2:9753939-9753989	HIPEpiC	eye:	n/a
47	chr2:9753939-9753989	HL-60	blood:	n/a
48	chr2:9753939-9753989	GM12892	blood:	n/a
49	chr2:9753939-9753989	HCF	heart:	n/a
50	chr2:9753939-9753989	Hela-S3	cervix:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:42142647..42144954-chr2:9753163..9755825,2	MCF-7	breast:
2	chr2:9694040..9697595-chr2:9752237..9755817,4	MCF-7	breast:
3	chr2:9277995..9280280-chr2:9751688..9754261,2	K562	blood:
4	chr2:9752399..9758466-chr2:9767981..9772630,10	MCF-7	breast:
5	chr2:9692463..9694432-chr2:9752498..9755143,2	MCF-7	breast:
6	chr2:9752582..9755080-chr2:9755247..9757680,2	MCF-7	breast:
7	chr2:9749693..9751303-chr2:9753003..9754631,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000207086	TF binding region
ENSG00000207086	CpG island
ENSG00000134308	Chromatin interaction
ENSG00000151694	Chromatin interaction
ENSG00000271855	Chromatin interaction
ENSG00000207086	Chromatin interaction
ENSG00000161654	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10495571	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10495572	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10495573	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11676903	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11692112	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11694314	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16867083	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17362734	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17362839	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17362902	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17453675	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17453724	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17453752	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55883249	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56372340	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57234614	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57407838	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60319753	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60726087	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62119391	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62119392	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62119393	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62119422	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62119423	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62119428	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62119429	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62119431	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62119433	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv580915	chr2:9308148-9844178	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9696800-9767600	Weak transcription	Gastric	stomach
2	chr2:9741400-9760000	Weak transcription	Fetal Kidney	kidney
3	chr2:9742200-9757000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:9742800-9757800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:9744600-9755200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:9744800-9766800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:9747800-9760200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:9748000-9757000	Enhancers	Brain Hippocampus Middle	brain
9	chr2:9748600-9755000	Weak transcription	Fetal Stomach	stomach
10	chr2:9748600-9756400	Enhancers	Brain Substantia Nigra	brain
11	chr2:9748600-9765600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:9748600-9766600	Weak transcription	Aorta	Aorta
13	chr2:9748600-9767600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:9748800-9758800	Weak transcription	Thymus	Thymus
15	chr2:9748800-9761200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:9748800-9763400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:9749000-9754400	Weak transcription	Fetal Intestine Small	intestine
18	chr2:9749000-9755000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:9749000-9756800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:9749000-9757800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:9749000-9764600	Weak transcription	Lung	lung
22	chr2:9749000-9769200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:9749200-9764000	Weak transcription	Fetal Brain Male	brain
24	chr2:9749200-9768000	Weak transcription	Stomach Mucosa	stomach
25	chr2:9749400-9762800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:9749600-9758000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr2:9749600-9768200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:9750000-9755800	Weak transcription	Brain Germinal Matrix	brain
29	chr2:9750000-9755800	Strong transcription	Dnd41	blood
30	chr2:9750000-9758000	Weak transcription	HUVEC	blood vessel
31	chr2:9750200-9758400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:9750200-9758600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:9750400-9754400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr2:9750400-9756000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:9750800-9754200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr2:9750800-9756400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:9751000-9754200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:9751000-9754200	Enhancers	Psoas Muscle	Psoas
39	chr2:9751000-9754400	Strong transcription	NHEK	skin
40	chr2:9751000-9757000	Enhancers	Colon Smooth Muscle	Colon
41	chr2:9751000-9757000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr2:9751000-9759000	Genic enhancers	A549	lung
43	chr2:9751200-9754200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:9751200-9754800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:9751200-9755200	Strong transcription	Primary B cells from cord blood	blood
46	chr2:9751400-9755000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:9751600-9755000	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr2:9751600-9756000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:9751600-9758800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:9751800-9756200	Enhancers	Fetal Heart	heart

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