Variant report

Variant	rs11685308
Chromosome Location	chr2:172183128-172183129
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr2:172182704-172183135	GM12878	blood:	n/a	n/a
2	GATA3	chr2:172183023-172183188	SH-SY5Y	brain:	n/a	n/a
3	MTA3	chr2:172182340-172183243	GM12878	blood:	n/a	n/a
4	RCOR1	chr2:172182837-172183457	GM12878	blood:	n/a	n/a
5	SMC3	chr2:172182579-172183345	GM12878	blood:	n/a	n/a
6	ATF2	chr2:172182437-172183219	GM12878	blood:	n/a	n/a
7	NFATC1	chr2:172182416-172183255	GM12878	blood:	n/a	n/a
8	FOXM1	chr2:172182440-172183209	GM12878	blood:	n/a	n/a
9	NFIC	chr2:172182366-172183506	GM12878	blood:	n/a	n/a
10	EP300	chr2:172182604-172183361	GM12878	blood:	n/a	n/a
11	RUNX3	chr2:172182443-172183181	GM12878	blood:	n/a	n/a
12	EP300	chr2:172182747-172183294	GM12878	blood:	n/a	n/a
13	IKZF1	chr2:172182487-172183322	GM12878	blood:	n/a	n/a
14	MTA3	chr2:172182541-172183140	GM12878	blood:	n/a	n/a
15	RUNX3	chr2:172182406-172183482	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:172182537-172183419	GM12878	blood:	n/a	n/a
17	BHLHE40	chr2:172182444-172183262	GM12878	blood:	n/a	n/a
18	STAT3	chr2:172182734-172183165	GM12878	blood:	n/a	n/a
19	CREB1	chr2:172182684-172183191	GM12878	blood:	n/a	n/a
20	YY1	chr2:172182825-172183188	GM12878	blood:	n/a	n/a
21	PML	chr2:172182477-172183435	GM12878	blood:	n/a	n/a
22	BCLAF1	chr2:172182422-172183177	GM12878	blood:	n/a	n/a
23	NFIC	chr2:172179384-172184108	GM12878	blood:	n/a	n/a
24	CREB1	chr2:172182655-172183288	GM12878	blood:	n/a	n/a
25	STAT5A	chr2:172182674-172183135	GM12878	blood:	n/a	n/a
26	MYC	chr2:172182817-172183305	H1-hESC	embryonic stem cell:	n/a	n/a
27	TBP	chr2:172182678-172183178	GM12878	blood:	n/a	n/a
28	IRF4	chr2:172182677-172183133	GM12878	blood:	n/a	n/a
29	ATF2	chr2:172182405-172183247	GM12878	blood:	n/a	n/a

No data

Variant related genes	Relation type
METTL8	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10173812	0.89[EUR][1000 genomes]
rs11674303	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11695531	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1178014	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12327994	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12989804	0.94[EUR][1000 genomes]
rs13023417	0.98[ASN][1000 genomes]
rs3731986	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs3731987	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57165050	1.00[ASN][1000 genomes]
rs6744452	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7349355	0.86[EUR][1000 genomes]
rs888521	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172169200-172193400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:172169800-172183200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:172170200-172192800	Weak transcription	Fetal Intestine Large	intestine
4	chr2:172171400-172190800	Weak transcription	Esophagus	oesophagus
5	chr2:172171800-172211600	Weak transcription	Fetal Intestine Small	intestine
6	chr2:172172600-172190600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:172172800-172190600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:172172800-172222400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:172173600-172186000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:172175400-172187600	Weak transcription	Fetal Muscle Leg	muscle
11	chr2:172175600-172188000	Weak transcription	Adipose Nuclei	Adipose
12	chr2:172175800-172183600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:172176000-172183400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:172176000-172184400	Weak transcription	NHDF-Ad	bronchial
15	chr2:172176000-172187800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:172176200-172183200	Weak transcription	Fetal Stomach	stomach
17	chr2:172176200-172183600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:172176200-172183800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:172176200-172198600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:172176400-172183400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:172177000-172183400	Weak transcription	Brain Hippocampus Middle	brain
22	chr2:172177200-172183200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:172177400-172183600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:172177600-172184400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:172177800-172183400	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:172178000-172183600	Weak transcription	Fetal Brain Male	brain
27	chr2:172178000-172190600	Weak transcription	Left Ventricle	heart
28	chr2:172178400-172183800	Weak transcription	Fetal Kidney	kidney
29	chr2:172180000-172183600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:172180000-172195800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:172180200-172185000	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr2:172180400-172184200	Enhancers	Primary T cells from cord blood	blood
33	chr2:172180400-172184800	Enhancers	H1 Cell Line	embryonic stem cell
34	chr2:172180600-172190800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:172180600-172203400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:172180800-172193000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:172180800-172198200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:172181000-172183400	Weak transcription	Fetal Thymus	thymus
39	chr2:172181000-172185000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:172181000-172188000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:172181000-172203800	Weak transcription	HMEC	breast
42	chr2:172181000-172221600	Weak transcription	K562	blood
43	chr2:172181200-172198000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:172181200-172204200	Weak transcription	NHEK	skin
45	chr2:172181400-172184400	Weak transcription	HepG2	liver
46	chr2:172181400-172185000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:172181800-172184800	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr2:172181800-172184800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr2:172181800-172184800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:172181800-172187200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links