Variant report

Variant	rs6717910
Chromosome Location	chr2:11917278-11917279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:11917156-11917325	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11885343..11888558-chr2:11916972..11921085,4	K562	blood:

Variant related genes	Relation type
LPIN1	TF binding region
ENSG00000230790	Chromatin interaction
ENSG00000134324	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1006538	0.89[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10169802	0.84[ASN][1000 genomes]
rs10192566	0.84[ASN][1000 genomes]
rs10205312	0.88[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs10205400	0.88[CHB][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs10207506	0.85[ASN][1000 genomes]
rs10208679	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10209969	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11676086	0.85[ASN][1000 genomes]
rs11693809	0.84[ASN][1000 genomes]
rs11897144	0.87[ASN][1000 genomes]
rs13407101	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13409154	0.85[ASN][1000 genomes]
rs13412852	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1469952	0.99[ASN][1000 genomes]
rs17603420	0.89[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs2278513	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs2358041	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2358042	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2358126	0.89[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs4076055	0.81[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4129757	0.88[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs4315495	0.85[ASN][1000 genomes]
rs62113306	0.81[ASN][1000 genomes]
rs6731096	0.81[ASN][1000 genomes]
rs6757892	0.90[ASN][1000 genomes]
rs72773994	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7561070	0.90[ASN][1000 genomes]
rs7595221	0.88[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs7607755	0.90[ASN][1000 genomes]
rs873358	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs893342	0.92[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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11895000-11918200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:11900600-11918000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:11901800-11918600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:11905200-11919000	Weak transcription	Stomach Mucosa	stomach
5	chr2:11906000-11917400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:11906400-11924600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:11906600-11924800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:11906800-11924600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:11908000-11919000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:11908600-11917600	Strong transcription	K562	blood
11	chr2:11909000-11919000	Strong transcription	HMEC	breast
12	chr2:11910000-11917400	Strong transcription	HepG2	liver
13	chr2:11910000-11918400	Strong transcription	Thymus	Thymus
14	chr2:11911800-11918200	Weak transcription	Small Intestine	intestine
15	chr2:11912000-11919000	Weak transcription	A549	lung
16	chr2:11912400-11917400	Weak transcription	Aorta	Aorta
17	chr2:11912400-11917400	Weak transcription	Spleen	Spleen
18	chr2:11912400-11917600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:11912400-11918200	Weak transcription	Colonic Mucosa	Colon
20	chr2:11912400-11919200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:11912600-11918400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:11912600-11918400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:11912600-11920400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:11913600-11919000	Weak transcription	Brain Substantia Nigra	brain
25	chr2:11914000-11919600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:11914600-11917400	Weak transcription	Psoas Muscle	Psoas
27	chr2:11914600-11918600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:11914800-11918400	Weak transcription	Primary B cells from cord blood	blood
29	chr2:11914800-11919200	Weak transcription	Fetal Brain Male	brain
30	chr2:11914800-11920200	Weak transcription	Fetal Lung	lung
31	chr2:11915000-11917400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:11915000-11917400	Weak transcription	Esophagus	oesophagus
33	chr2:11915000-11917400	Weak transcription	Gastric	stomach
34	chr2:11915000-11917400	Weak transcription	Lung	lung
35	chr2:11915000-11917400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:11915000-11918200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:11915000-11918400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:11915000-11918600	Weak transcription	Fetal Brain Female	brain
39	chr2:11915000-11918800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr2:11915000-11919200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:11915000-11919200	Weak transcription	Right Ventricle	heart
42	chr2:11915000-11923200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr2:11915200-11917400	Weak transcription	Placenta	Placenta
44	chr2:11915200-11918400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr2:11915200-11919000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:11915200-11919200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:11915200-11919600	Weak transcription	Ovary	ovary
48	chr2:11915400-11918400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr2:11915400-11918800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr2:11915400-11919000	Weak transcription	Fetal Heart	heart

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