Variant report

Variant	rs6704590
Chromosome Location	chr2:172878554-172878555
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172857904..172859439-chr2:172876035..172878668,2	K562	blood:
2	chr2:172877706..172879734-chr2:172884622..172888221,3	K562	blood:
3	chr2:172864480..172870614-chr2:172875986..172878962,8	K562	blood:
4	chr2:172862481..172869340-chr2:172872333..172878575,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172878	Chromatin interaction
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1008152	0.88[AMR][1000 genomes]
rs12622895	0.85[CEU][hapmap]
rs17428076	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17428174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17500114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17615262	0.90[CEU][hapmap]
rs3736499	0.84[CEU][hapmap]
rs3765166	0.85[CEU][hapmap]
rs3821093	0.84[CEU][hapmap]
rs55863868	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56218609	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62183804	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183808	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183809	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183852	0.88[AMR][1000 genomes]
rs6737876	0.88[AMR][1000 genomes]
rs6749895	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72892835	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72892859	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs788161	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs788164	0.85[CEU][hapmap]
rs788168	0.85[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv3031	chr2:172867462-172884232	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172865200-172886600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:172865600-172897400	Weak transcription	Primary T cells from cord blood	blood
3	chr2:172865800-172886400	Weak transcription	Fetal Intestine Small	intestine
4	chr2:172865800-172886600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:172866000-172886800	Weak transcription	HSMMtube	muscle
6	chr2:172866800-172882600	Weak transcription	K562	blood
7	chr2:172874200-172886400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:172875200-172878800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr2:172875800-172879200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr2:172876400-172878800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:172876600-172878800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr2:172876800-172878600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr2:172876800-172878600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr2:172876800-172878800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr2:172877000-172878600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:172877000-172878600	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr2:172877000-172878600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr2:172877000-172878600	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr2:172877000-172878800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr2:172877000-172878800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:172877000-172878800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:172877000-172878800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr2:172877200-172878600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:172877200-172878600	Enhancers	Fetal Brain Female	brain
25	chr2:172877200-172878600	Enhancers	Ovary	ovary
26	chr2:172877200-172878600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr2:172877200-172878600	Enhancers	Spleen	Spleen
28	chr2:172877400-172878600	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr2:172877400-172878800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:172877600-172878600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr2:172877800-172878600	Enhancers	H9 Cell Line	embryonic stem cell
32	chr2:172877800-172878600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr2:172877800-172878600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:172877800-172878600	Enhancers	Pancreas	Pancrea
35	chr2:172877800-172878600	Enhancers	Psoas Muscle	Psoas
36	chr2:172877800-172878600	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr2:172878000-172878600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:172878000-172878600	Enhancers	Primary B cells from cord blood	blood
39	chr2:172878000-172878600	Enhancers	Gastric	stomach
40	chr2:172878200-172878600	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr2:172878200-172878600	Flanking Active TSS	GM12878-XiMat	blood
42	chr2:172878200-172884800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:172878200-172886400	Weak transcription	Fetal Muscle Leg	muscle
44	chr2:172878400-172878600	Enhancers	Primary B cells from peripheral blood	blood
45	chr2:172878400-172886000	Weak transcription	HepG2	liver

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