Variant report

Variant	rs7706876
Chromosome Location	chr5:179480172-179480173
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179480070..179481635-chr5:179485420..179487501,2	K562	blood:
2	chr5:179232497..179234437-chr5:179477611..179480495,2	K562	blood:
3	chr5:179474557..179476078-chr5:179480075..179482538,2	MCF-7	breast:
4	chr5:179477454..179480172-chr5:179480653..179484113,3	MCF-7	breast:
5	chr5:179473631..179475664-chr5:179477740..179480217,2	K562	blood:
6	chr5:179474524..179477374-chr5:179479073..179481485,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161011	Chromatin interaction
ENSG00000161013	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10041471	0.84[ASN][1000 genomes]
rs10045947	0.81[CEU][hapmap];0.84[MKK][hapmap]
rs10054764	0.85[EUR][1000 genomes]
rs10058085	0.85[EUR][1000 genomes]
rs10073876	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs10075114	0.88[ASN][1000 genomes]
rs10075627	0.81[CEU][hapmap]
rs11948891	0.92[EUR][1000 genomes]
rs11954181	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs13161042	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1348523	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1867447	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2115042	0.85[EUR][1000 genomes]
rs28754309	0.92[EUR][1000 genomes]
rs34044107	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34434279	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs59446142	0.95[ASN][1000 genomes]
rs62404973	0.85[EUR][1000 genomes]
rs62405022	0.92[EUR][1000 genomes]
rs62405023	0.92[EUR][1000 genomes]
rs6882944	0.90[ASN][1000 genomes]
rs73348273	0.85[EUR][1000 genomes]
rs7448914	0.85[EUR][1000 genomes]
rs9329092	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer 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	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer 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	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7706876	RUFY1	cis	cerebellum	SCAN
rs7706876	NOP16	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:179461800-179483600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:179463800-179482200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:179464800-179483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:179465400-179484200	Weak transcription	Aorta	Aorta
6	chr5:179467400-179483200	Weak transcription	HSMM	muscle
7	chr5:179472400-179496600	Weak transcription	Stomach Mucosa	stomach
8	chr5:179473200-179482000	Enhancers	Brain Substantia Nigra	brain
9	chr5:179473400-179481600	Enhancers	Brain Anterior Caudate	brain
10	chr5:179473800-179484000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:179473800-179488000	Weak transcription	Fetal Stomach	stomach
12	chr5:179474000-179484000	Enhancers	Brain Cingulate Gyrus	brain
13	chr5:179474000-179496200	Weak transcription	Primary B cells from cord blood	blood
14	chr5:179475200-179481600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr5:179475800-179483400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:179476000-179481600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:179476000-179484400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:179476000-179497800	Weak transcription	Lung	lung
19	chr5:179476400-179481400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr5:179476400-179486200	Weak transcription	Ovary	ovary
21	chr5:179476400-179487000	Weak transcription	Fetal Muscle Leg	muscle
22	chr5:179476400-179496800	Weak transcription	Right Ventricle	heart
23	chr5:179476800-179480200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr5:179477400-179480200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:179477400-179480200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr5:179477400-179481200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:179477400-179483800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr5:179477400-179494000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr5:179477400-179495000	Weak transcription	Gastric	stomach
30	chr5:179477600-179480200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr5:179477600-179483600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:179477600-179486200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:179477800-179481400	Weak transcription	HepG2	liver
34	chr5:179478000-179480200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr5:179478000-179482400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:179478000-179496800	Weak transcription	Right Atrium	heart
37	chr5:179478200-179480400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr5:179478200-179481200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr5:179478200-179481200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr5:179478400-179484200	Enhancers	Brain Hippocampus Middle	brain
41	chr5:179478600-179480400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:179478600-179480600	Enhancers	Brain Angular Gyrus	brain
43	chr5:179478600-179481400	Enhancers	Brain Germinal Matrix	brain
44	chr5:179478800-179480200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:179478800-179493800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr5:179479000-179480400	Enhancers	Fetal Brain Male	brain
47	chr5:179479000-179481400	Enhancers	Colon Smooth Muscle	Colon
48	chr5:179479000-179481400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr5:179479000-179481600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr5:179479000-179481600	Enhancers	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links