Variant report

Variant	rs928603
Chromosome Location	chr10:99183402-99183403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr10:99182738-99184115	NB4	blood:	n/a	n/a
2	CTCF	chr10:99183260-99183410	HBMEC	blood vessel:	n/a	n/a
3	POLR2A	chr10:99183125-99184539	K562	blood:	n/a	n/a
4	CTCF	chr10:99183260-99183410	HEEpiC	esophagus:	n/a	n/a
5	CTCF	chr10:99183260-99183410	GM12878	blood:	n/a	n/a
6	CTCF	chr10:99183280-99183430	GM12873	blood:	n/a	n/a
7	JUND	chr10:99182618-99183406	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr10:99183260-99183410	GM06990	blood:	n/a	n/a
9	MYC	chr10:99183320-99183874	NB4	blood:	n/a	n/a
10	CTCF	chr10:99183280-99183430	NB4	blood:	n/a	n/a
11	CTCF	chr10:99183260-99183410	GM12864	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:99183360-99183410	HIPEpiC	eye:	n/a
2	chr10:99183360-99183410	A549	lung:	n/a
3	chr10:99183360-99183410	IMR90	lung:	fetal
4	chr10:99183360-99183410	HRCEpiC	kidney:	n/a
5	chr10:99183360-99183410	HL-60	blood:	n/a
6	chr10:99183360-99183410	SK-N-SH_RA	brain:	n/a
7	chr10:99183360-99183410	HRPEpiC	eye:	n/a
8	chr10:99183360-99183410	HUVEC	blood vessel:	n/a
9	chr10:99183360-99183410	HCPEpiC	choroid plexus:	n/a
10	chr10:99183360-99183410	GM12891	blood:	n/a
11	chr10:99183360-99183410	Jurkat	blood:	n/a
12	chr10:99183360-99183410	NH-A	brain:	n/a
13	chr10:99183360-99183410	AoSMC	blood vessel:	n/a
14	chr10:99183360-99183410	Hela-S3	cervix:	n/a
15	chr10:99183360-99183410	SK-N-SH	brain:	n/a
16	chr10:99183360-99183410	HCT-116	colon:	n/a
17	chr10:99183360-99183410	Hepatocyte	liver:	n/a
18	chr10:99183360-99183410	NHBE	bronchial:	n/a
19	chr10:99183360-99183410	HAEpiC	amniotic membrane:	n/a
20	chr10:99183360-99183410	ProgFib	skin:	n/a
21	chr10:99183360-99183410	HepG2	liver:	n/a
22	chr10:99183360-99183410	HEK293	kidney:	embryo
23	chr10:99183360-99183410	ECC-1	luminal epithelium:	n/a
24	chr10:99183360-99183410	RPTEC	kidney:	n/a
25	chr10:99183360-99183410	BJ	skin:	n/a
26	chr10:99183360-99183410	AG10803	skin:	n/a
27	chr10:99183360-99183410	PFSK-1	brain:	n/a
28	chr10:99183360-99183410	MCF10A-Er-Src	breast:	n/a
29	chr10:99183360-99183410	HCF	heart:	n/a
30	chr10:99183360-99183410	U87	brain:	n/a
31	chr10:99183360-99183410	AG09309	skin:	n/a
32	chr10:99183360-99183410	ovcar-3	ovarian:	n/a
33	chr10:99183360-99183410	AG09319	gingival:	n/a
34	chr10:99183360-99183410	GM12892	blood:	n/a
35	chr10:99183360-99183410	AG04450	lung:	fetal
36	chr10:99183360-99183410	NT2-D1	testis:	n/a
37	chr10:99183360-99183410	BE2_C	brain:	n/a
38	chr10:99183360-99183410	K562	blood:	n/a
39	chr10:99183360-99183410	NHDF-neo	bronchial:	n/a
40	chr10:99183360-99183410	SAEC	small airway:	n/a
41	chr10:99183360-99183410	LNCaP	prostate:	n/a
42	chr10:99183360-99183410	Caco-2	colon:	n/a
43	chr10:99183360-99183410	HPAEpiC	pulmonary alveolar:	n/a
44	chr10:99183360-99183410	CMK	blood:	n/a
45	chr10:99183360-99183410	H1-hESC	embryonic stem cell:	embryo
46	chr10:99183360-99183410	PrEC	prostate:	n/a
47	chr10:99183360-99183410	PANC-1	pancreas:	n/a
48	chr10:99183360-99183410	HMEC	breast:	n/a
49	chr10:99183360-99183410	GM19239	blood:	n/a
50	chr10:99183360-99183410	MCF-7	breast:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99028369..99030720-chr10:99181832..99184163,2	MCF-7	breast:
2	chr10:99176624..99178423-chr10:99181529..99184157,2	K562	blood:
3	chr10:99176991..99182775-chr10:99183273..99189892,9	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL355490.1-1	chr10:99176179-99185666	NONHSAT015863

No data

Variant related genes	Relation type
ENSG00000200737	TF binding region
PGAM1	TF binding region
ENSG00000200737	CpG island
PGAM1	CpG island
ENSG00000213390	Chromatin interaction
ENSG00000200737	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10882905	1.00[YRI][hapmap]
rs12569570	0.95[AFR][1000 genomes]
rs1334891	0.84[ASW][hapmap]
rs2297666	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4304701	0.91[CHB][hapmap]
rs4919096	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7081796	0.86[CHB][hapmap]
rs7090847	0.87[ASN][1000 genomes]
rs764223	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467440	chr10:99134784-99204791	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv552025	chr10:99134784-99204791	Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99161600-99185200	Weak transcription	Pancreas	Pancrea
2	chr10:99167400-99185200	Weak transcription	Fetal Lung	lung
3	chr10:99167400-99185400	Weak transcription	Gastric	stomach
4	chr10:99167600-99185200	Weak transcription	Fetal Intestine Small	intestine
5	chr10:99167600-99185200	Weak transcription	Left Ventricle	heart
6	chr10:99171400-99185200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:99174000-99185000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:99174200-99184800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr10:99174200-99185000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr10:99175400-99185000	Weak transcription	Brain Germinal Matrix	brain
11	chr10:99176600-99185200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr10:99177800-99185200	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr10:99178200-99185200	Weak transcription	Ovary	ovary
14	chr10:99178400-99185000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr10:99178400-99185200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr10:99178400-99185200	Weak transcription	Right Ventricle	heart
17	chr10:99178400-99185200	Weak transcription	Small Intestine	intestine
18	chr10:99178600-99184800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr10:99178800-99185400	Weak transcription	Aorta	Aorta
20	chr10:99179000-99184800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr10:99179000-99184800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr10:99179000-99185200	Weak transcription	Lung	lung
23	chr10:99179200-99184600	Weak transcription	Placenta	Placenta
24	chr10:99179200-99184800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr10:99179200-99184800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr10:99179200-99185000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr10:99179200-99185000	Weak transcription	Adipose Nuclei	Adipose
28	chr10:99179200-99185000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr10:99179200-99185200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr10:99179200-99185200	Weak transcription	Colon Smooth Muscle	Colon
31	chr10:99179200-99185200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr10:99179200-99185200	Weak transcription	Fetal Intestine Large	intestine
33	chr10:99179200-99185200	Weak transcription	Fetal Kidney	kidney
34	chr10:99179200-99185200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr10:99179200-99185200	Weak transcription	Stomach Mucosa	stomach
36	chr10:99179400-99184800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr10:99179400-99184800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr10:99179400-99184800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr10:99179400-99184800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr10:99179400-99185000	Weak transcription	Primary T cells from cord blood	blood
41	chr10:99179400-99185000	Weak transcription	Thymus	Thymus
42	chr10:99179400-99185200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr10:99179600-99184600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr10:99179600-99185000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr10:99179600-99185200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr10:99179800-99184600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr10:99179800-99184600	Strong transcription	Fetal Stomach	stomach
48	chr10:99179800-99185200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr10:99180800-99185000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr10:99181400-99185000	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links