Variant report

Variant	rs72786623
Chromosome Location	chr2:10198197-10198198
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr2:10197755-10198239	HepG2	liver:	n/a	n/a
2	ELF1	chr2:10197353-10198284	MCF-7	breast:	n/a	n/a
3	TEAD4	chr2:10197796-10198248	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr2:10197788-10198235	H1-hESC	embryonic stem cell:	n/a	n/a
5	EGR1	chr2:10197191-10198320	HCT-116	colon:	n/a	n/a
6	SIN3A	chr2:10197355-10198254	H1-hESC	embryonic stem cell:	n/a	n/a
7	EGR1	chr2:10197113-10198319	HCT-116	colon:	n/a	n/a
8	CBX3	chr2:10197241-10198205	K562	blood:	n/a	n/a
9	POLR2A	chr2:10198032-10198232	GM12878	blood:	n/a	n/a
10	CTBP2	chr2:10197409-10198548	H1-hESC	embryonic stem cell:	n/a	n/a
11	NR2F2	chr2:10197137-10198530	K562	blood:	n/a	n/a
12	CTCF	chr2:10198183-10198657	K562	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:10183033..10185119-chr2:10198033..10200377,2	MCF-7	breast:
2	chr2:10196086..10198702-chr2:10218422..10220435,2	MCF-7	breast:
3	chr2:10197998..10200342-chr2:10271933..10274475,2	K562	blood:
4	chr2:10188186..10190584-chr2:10195976..10198794,3	K562	blood:
5	chr2:10197205..10199303-chr2:10204437..10207359,3	K562	blood:
6	chr2:10090704..10092737-chr2:10197236..10199452,2	MCF-7	breast:
7	chr2:9769621..9772797-chr2:10196193..10199628,3	MCF-7	breast:
8	chr2:9282583..9283382-chr2:10198006..10198928,2	K562	blood:
9	chr2:10197111..10198672-chr2:10588084..10590200,2	K562	blood:
10	chr2:10182483..10186583-chr2:10197411..10199224,5	K562	blood:
11	chr2:10195492..10201555-chr2:10257340..10265451,9	K562	blood:
12	chr2:10196236..10199023-chr2:10202706..10204549,2	K562	blood:
13	chr2:10183017..10185520-chr2:10196583..10199380,4	MCF-7	breast:
14	chr2:9769286..9771106-chr2:10196629..10198353,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000271787	TF binding region
ENSG00000134308	Chromatin interaction
ENSG00000240980	Chromatin interaction
ENSG00000272524	Chromatin interaction
ENSG00000134317	Chromatin interaction
ENSG00000172059	Chromatin interaction
ENSG00000171848	Chromatin interaction
ENSG00000257135	Chromatin interaction
ENSG00000115758	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10177872	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929632	1.00[ASN][1000 genomes]
rs11886661	1.00[ASN][1000 genomes]
rs13400128	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935840	1.00[ASN][1000 genomes]
rs4302193	1.00[ASN][1000 genomes]
rs4321336	1.00[ASN][1000 genomes]
rs4485541	1.00[ASN][1000 genomes]
rs4569449	1.00[ASN][1000 genomes]
rs4669527	1.00[ASN][1000 genomes]
rs6432058	1.00[ASN][1000 genomes]
rs6432060	1.00[ASN][1000 genomes]
rs72786624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587317	1.00[ASN][1000 genomes]
rs7587529	1.00[ASN][1000 genomes]
rs7602408	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1007965	chr2:10154960-10276125	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1014790	chr2:10156968-10274855	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv999019	chr2:10157762-10273232	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
7	nsv873633	chr2:10175442-10266563	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
8	nsv828308	chr2:10175525-10200328	Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv1010706	chr2:10189219-10266995	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10185000-10200400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:10189000-10200000	Weak transcription	Psoas Muscle	Psoas
3	chr2:10192800-10200600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:10193600-10200200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:10193600-10200400	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:10193600-10218400	Weak transcription	Brain Angular Gyrus	brain
7	chr2:10194000-10205600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:10194400-10200400	Weak transcription	Brain Substantia Nigra	brain
9	chr2:10194400-10203000	Weak transcription	Aorta	Aorta
10	chr2:10194600-10200600	Weak transcription	Brain Anterior Caudate	brain
11	chr2:10194600-10215600	Weak transcription	Fetal Kidney	kidney
12	chr2:10194800-10200400	Weak transcription	Fetal Brain Female	brain
13	chr2:10195400-10200000	Weak transcription	Liver	Liver
14	chr2:10195400-10200400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:10196600-10198200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:10196800-10198200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:10196800-10198200	Enhancers	Adipose Nuclei	Adipose
18	chr2:10196800-10198400	Enhancers	Spleen	Spleen
19	chr2:10196800-10198600	Enhancers	Lung	lung
20	chr2:10197000-10198200	Flanking Active TSS	HMEC	breast
21	chr2:10197000-10198400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr2:10197000-10200200	Weak transcription	Left Ventricle	heart
23	chr2:10197000-10203800	Weak transcription	Gastric	stomach
24	chr2:10197200-10198200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:10197200-10198200	Enhancers	Colon Smooth Muscle	Colon
26	chr2:10197200-10198400	Enhancers	Stomach Mucosa	stomach
27	chr2:10197400-10198200	Active TSS	H9 Cell Line	embryonic stem cell
28	chr2:10197400-10198200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:10197400-10198200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:10197400-10198200	Enhancers	Esophagus	oesophagus
31	chr2:10197400-10198200	Flanking Active TSS	Placenta	Placenta
32	chr2:10197400-10198200	Enhancers	Right Ventricle	heart
33	chr2:10197400-10198400	Flanking Active TSS	NHEK	skin
34	chr2:10197600-10198200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
35	chr2:10197600-10205400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:10197800-10198200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:10197800-10198200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:10197800-10198200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:10197800-10198200	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr2:10197800-10198200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr2:10197800-10198200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr2:10197800-10198200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:10197800-10198200	Flanking Active TSS	Ovary	ovary
44	chr2:10197800-10198200	Genic enhancers	Pancreas	Pancrea
45	chr2:10197800-10198200	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr2:10197800-10198200	Enhancers	HSMM	muscle
47	chr2:10197800-10198200	Flanking Active TSS	K562	blood
48	chr2:10197800-10198200	Enhancers	NHLF	lung
49	chr2:10197800-10198400	Flanking Active TSS	HepG2	liver
50	chr2:10197800-10198400	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links