Variant report

Variant	rs16953709
Chromosome Location	chr13:97647236-97647237
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr13:97646850-97647263	HEK293	kidney:	n/a	n/a
2	TEAD4	chr13:97647215-97647587	H1-hESC	embryonic stem cell:	n/a	n/a
3	E2F6	chr13:97645896-97647249	H1-hESC	embryonic stem cell:	n/a	chr13:97646807-97646822 chr13:97646805-97646815 chr13:97646806-97646814 chr13:97646809-97646818 chr13:97646810-97646817 chr13:97646806-97646814 chr13:97646810-97646817 chr13:97646806-97646813 chr13:97646806-97646817 chr13:97646807-97646821 chr13:97646810-97646817 chr13:97646805-97646816

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:97647222-97647272	GM12892	blood:	n/a
2	chr13:97647222-97647272	Jurkat	blood:	n/a
3	chr13:97647222-97647272	RPTEC	kidney:	n/a
4	chr13:97647222-97647272	HMEC	breast:	n/a
5	chr13:97647222-97647272	AG09319	gingival:	n/a
6	chr13:97647222-97647272	SAEC	small airway:	n/a
7	chr13:97647222-97647272	HEK293	kidney:	embryo
8	chr13:97647222-97647272	NH-A	brain:	n/a
9	chr13:97647222-97647272	AG10803	skin:	n/a
10	chr13:97647222-97647272	HL-60	blood:	n/a
11	chr13:97647222-97647272	AoSMC	blood vessel:	n/a
12	chr13:97647222-97647272	Caco-2	colon:	n/a
13	chr13:97647222-97647272	Hela-S3	cervix:	n/a
14	chr13:97647222-97647272	NHDF-neo	bronchial:	n/a
15	chr13:97647222-97647272	U87	brain:	n/a
16	chr13:97647222-97647272	HIPEpiC	eye:	n/a
17	chr13:97647222-97647272	ovcar-3	ovarian:	n/a
18	chr13:97647222-97647272	HCF	heart:	n/a
19	chr13:97647222-97647272	BJ	skin:	n/a
20	chr13:97647222-97647272	BE2_C	brain:	n/a
21	chr13:97647222-97647272	GM19239	blood:	n/a
22	chr13:97647222-97647272	NT2-D1	testis:	n/a
23	chr13:97647222-97647272	LNCaP	prostate:	n/a
24	chr13:97647222-97647272	SK-N-SH	brain:	n/a
25	chr13:97647222-97647272	SK-N-SH_RA	brain:	n/a
26	chr13:97647222-97647272	MCF-7	breast:	n/a
27	chr13:97647222-97647272	GM06990	blood:	n/a
28	chr13:97647222-97647272	HUVEC	blood vessel:	n/a
29	chr13:97647222-97647272	GM12891	blood:	n/a
30	chr13:97647222-97647272	NB4	blood:	n/a
31	chr13:97647222-97647272	SKMC	muscle:	n/a
32	chr13:97647222-97647272	AG04449	skin:	fetal
33	chr13:97647222-97647272	HRPEpiC	eye:	n/a
34	chr13:97647222-97647272	PFSK-1	brain:	n/a
35	chr13:97647222-97647272	H1-hESC	embryonic stem cell:	embryo
36	chr13:97647222-97647272	HNPCEpiC	eye:	n/a
37	chr13:97647222-97647272	HCPEpiC	choroid plexus:	n/a
38	chr13:97647222-97647272	ProgFib	skin:	n/a
39	chr13:97647222-97647272	AG09309	skin:	n/a
40	chr13:97647222-97647272	HCT-116	colon:	n/a
41	chr13:97647222-97647272	A549	lung:	n/a
42	chr13:97647222-97647272	PrEC	prostate:	n/a
43	chr13:97647222-97647272	SK-N-MC	brain:	n/a
44	chr13:97647222-97647272	NHBE	bronchial:	n/a
45	chr13:97647222-97647272	T-47D	breast:	n/a
46	chr13:97647222-97647272	HEEpiC	esophagus:	n/a
47	chr13:97647222-97647272	MCF10A-Er-Src	breast:	n/a
48	chr13:97647222-97647272	AG04450	lung:	fetal
49	chr13:97647222-97647272	K562	blood:	n/a
50	chr13:97647222-97647272	HCM	heart:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HS6ST3-3	chr13:97646606-97649813	NONHSAT034817

No data

Variant related genes	Relation type
OXGR1	TF binding region
OXGR1	CpG island

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10162251	0.92[EUR][1000 genomes]
rs10467249	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1604445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16953867	1.00[GIH][hapmap]
rs60668201	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60711187	0.92[EUR][1000 genomes]
rs7323760	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7333674	1.00[EUR][1000 genomes]
rs7993335	0.85[EUR][1000 genomes]
rs8001111	0.92[EUR][1000 genomes]
rs9582094	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9584459	1.00[EUR][1000 genomes]
rs9584461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9584462	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9584464	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9584465	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9584504	1.00[CEU][hapmap]

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	nsv832693	chr13:97594845-97777481	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16953709	HS6ST3	cis	lymphoblastoid	seeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:97645800-97647400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr13:97645800-97647400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr13:97645800-97647400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr13:97646000-97647400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:97646000-97647400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
6	chr13:97646400-97647400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
7	chr13:97646600-97647400	Bivalent Enhancer	Placenta	Placenta
8	chr13:97647000-97647400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
9	chr13:97647000-97647400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
10	chr13:97647000-97647400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
11	chr13:97647000-97647400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr13:97647000-97647400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
13	chr13:97647000-97647400	Bivalent Enhancer	Adipose Nuclei	Adipose
14	chr13:97647000-97647400	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
15	chr13:97647000-97647400	Bivalent Enhancer	Rectal Smooth Muscle	rectum
16	chr13:97647200-97647400	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr13:97647200-97647400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:97647200-97647400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
19	chr13:97647200-97647400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr13:97647200-97647400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr13:97647200-97647400	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr13:97647200-97647400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr13:97647200-97647400	Enhancers	Brain Anterior Caudate	brain
24	chr13:97647200-97647400	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr13:97647200-97647400	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
26	chr13:97647200-97647400	Bivalent Enhancer	Colon Smooth Muscle	Colon
27	chr13:97647200-97647400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
28	chr13:97647200-97647400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr13:97647200-97647400	Enhancers	Spleen	Spleen
30	chr13:97647200-97647600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr13:97647200-97648000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
32	chr13:97647200-97653400	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links