Variant report

Variant	rs17617710
Chromosome Location	chr5:179206107-179206108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179204742..179207120-chr5:179244847..179246652,2	K562	blood:
2	chr5:179196549..179199381-chr5:179205850..179207537,2	MCF-7	breast:
3	chr5:179199509..179202670-chr5:179203862..179207136,4	MCF-7	breast:
4	chr5:179205957..179207615-chr5:179218348..179219920,2	MCF-7	breast:
5	chr5:179203507..179207509-chr5:179245865..179250105,5	K562	blood:
6	chr5:179199669..179202266-chr5:179204889..179207881,3	K562	blood:
7	chr5:179199705..179202070-chr5:179203658..179206224,2	MCF-7	breast:
8	chr5:179205387..179207447-chr5:179218747..179220491,2	K562	blood:
9	chr5:179205290..179207447-chr5:179218747..179221079,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000213316	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000161011	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11738269	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738720	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739042	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740569	0.86[ASN][1000 genomes]
rs11741570	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743232	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11744616	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746924	0.86[ASN][1000 genomes]
rs11747496	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12522263	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1469020	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1469021	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17617068	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs34057110	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3756614	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3797762	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797776	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41458244	0.97[ASN][1000 genomes]
rs4700838	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700840	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55654737	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55827522	0.96[ASN][1000 genomes]
rs55975622	0.91[ASN][1000 genomes]
rs56309143	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56335144	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs58386410	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62404347	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62406176	0.90[ASN][1000 genomes]
rs62406177	0.90[ASN][1000 genomes]
rs62406178	0.90[ASN][1000 genomes]
rs62406181	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62406187	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406219	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406223	0.94[ASN][1000 genomes]
rs6601067	0.86[ASN][1000 genomes]
rs6601072	0.92[ASN][1000 genomes]
rs6639	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6860716	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6887507	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893300	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs6895902	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72807339	0.83[ASN][1000 genomes]
rs730012	0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs7444006	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7447159	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7704520	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7705530	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709723	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7715356	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7734102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7735702	0.80[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[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	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv518964	chr5:179193598-179227286	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
7	nsv883275	chr5:179193598-179267783	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
8	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
9	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17617710	C5orf45	cis	parietal	SCAN
rs17617710	CANX	cis	parietal	SCAN
rs17617710	TRIM52	cis	parietal	SCAN
rs17617710	CANX	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179190800-179207600	Strong transcription	Dnd41	blood
2	chr5:179191200-179210400	Strong transcription	Thymus	Thymus
3	chr5:179192000-179207800	Strong transcription	Fetal Thymus	thymus
4	chr5:179192200-179206200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:179192200-179206200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr5:179192200-179206400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr5:179192200-179206400	Strong transcription	HepG2	liver
8	chr5:179192200-179207600	Strong transcription	Fetal Lung	lung
9	chr5:179192200-179207800	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr5:179192200-179208000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:179192200-179210400	Strong transcription	Brain Germinal Matrix	brain
12	chr5:179192400-179206200	Strong transcription	GM12878-XiMat	blood
13	chr5:179192400-179207600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:179192400-179207600	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr5:179192600-179209800	Strong transcription	Primary T cells from cord blood	blood
16	chr5:179192800-179207200	Strong transcription	Fetal Muscle Leg	muscle
17	chr5:179192800-179209800	Strong transcription	Fetal Brain Female	brain
18	chr5:179193000-179210400	Strong transcription	Fetal Stomach	stomach
19	chr5:179193400-179207600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:179193400-179207800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:179193400-179208000	Strong transcription	Lung	lung
22	chr5:179193600-179206800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr5:179193600-179207600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:179193600-179207600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:179193600-179209600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:179193800-179206200	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr5:179193800-179206200	Strong transcription	HSMMtube	muscle
28	chr5:179193800-179207000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:179193800-179207400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr5:179193800-179207600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr5:179193800-179207800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr5:179193800-179207800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:179193800-179207800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr5:179193800-179208400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:179193800-179209400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:179193800-179209600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr5:179194200-179207400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:179194200-179207600	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr5:179194400-179206200	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:179194400-179207400	Strong transcription	Osteobl	bone
41	chr5:179194400-179207600	Strong transcription	Fetal Intestine Large	intestine
42	chr5:179194400-179207800	Strong transcription	Stomach Smooth Muscle	stomach
43	chr5:179194400-179208000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr5:179194600-179207800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:179194600-179210400	Strong transcription	Fetal Intestine Small	intestine
46	chr5:179194800-179207800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:179195400-179207200	Strong transcription	NHLF	lung
48	chr5:179195400-179207800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:179195800-179207600	Strong transcription	Pancreas	Pancrea
50	chr5:179195800-179208600	Strong transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links