Variant report

Variant	rs2170297
Chromosome Location	chr18:8829035-8829036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr18:8828472-8829135	NB4	blood:	n/a	n/a
2	RCOR1	chr18:8829020-8829122	K562	blood:	n/a	n/a
3	POLR2A	chr18:8827818-8831815	A549	lung:	n/a	n/a
4	MYC	chr18:8828536-8829121	NB4	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:8814066..8816178-chr18:8827038..8829489,2	MCF-7	breast:
2	chr18:8824115..8826531-chr18:8827743..8829537,2	K562	blood:
3	chr18:8811800..8814027-chr18:8828747..8831141,2	K562	blood:
4	chr18:8827382..8829668-chr18:8830158..8832451,3	K562	blood:

No data

Variant related genes	Relation type
SOGA2	TF binding region
ENSG00000168502	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10432143	0.88[ASN][1000 genomes]
rs11081410	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11665124	1.00[GIH][hapmap]
rs12956170	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs12956773	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs12957034	1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs12962890	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs1564484	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs16954398	0.81[ASN][1000 genomes]
rs2242273	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34740257	0.96[ASN][1000 genomes]
rs35950206	0.86[ASN][1000 genomes]
rs4798691	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs595802	0.90[CHB][hapmap]
rs71362044	0.86[ASN][1000 genomes]
rs7233770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7240816	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064883	chr18:8709670-9133224	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv833584	chr18:8728616-8904213	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv909363	chr18:8775184-8858086	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8789400-8829800	Weak transcription	Brain Anterior Caudate	brain
2	chr18:8801200-8834800	Weak transcription	Esophagus	oesophagus
3	chr18:8802400-8830000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr18:8805400-8829200	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr18:8807800-8835200	Weak transcription	Right Ventricle	heart
6	chr18:8817000-8830400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr18:8817200-8834800	Weak transcription	Psoas Muscle	Psoas
8	chr18:8817800-8830800	Strong transcription	Fetal Stomach	stomach
9	chr18:8821400-8830000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr18:8821400-8831600	Weak transcription	Aorta	Aorta
11	chr18:8821400-8834600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr18:8821600-8834800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr18:8822000-8829400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr18:8822400-8836800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr18:8823200-8831800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr18:8825400-8829800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr18:8825400-8831600	Weak transcription	Ovary	ovary
18	chr18:8825600-8834000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr18:8825600-8835200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr18:8825800-8830400	Weak transcription	HMEC	breast
21	chr18:8825800-8833200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr18:8825800-8835000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr18:8826000-8833400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr18:8826200-8830000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr18:8826200-8835000	Weak transcription	Placenta	Placenta
26	chr18:8826200-8839600	Weak transcription	Brain Angular Gyrus	brain
27	chr18:8826400-8830400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr18:8826400-8832200	Weak transcription	Fetal Intestine Small	intestine
29	chr18:8826400-8834800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr18:8826400-8841600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr18:8826600-8829400	Enhancers	Stomach Mucosa	stomach
32	chr18:8826600-8830000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr18:8826800-8835200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr18:8827000-8831800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr18:8827200-8830400	Weak transcription	NHEK	skin
36	chr18:8827200-8834800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr18:8827400-8829200	Enhancers	Gastric	stomach
38	chr18:8827400-8830800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr18:8827400-8832600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr18:8827400-8834800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr18:8827400-8835000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr18:8827600-8829200	Enhancers	Fetal Brain Male	brain
43	chr18:8827600-8829600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr18:8827600-8831600	Weak transcription	NH-A	brain
45	chr18:8827600-8832800	Weak transcription	HSMMtube	muscle
46	chr18:8827600-8834200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr18:8827600-8834600	Weak transcription	Osteobl	bone
48	chr18:8827600-8834800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr18:8827600-8835200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr18:8827600-8839000	Weak transcription	Pancreas	Pancrea

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