Variant report

Variant	rs7719611
Chromosome Location	chr5:59988547-59988548
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:59982671..59990838-chr5:59991133..59997951,12	MCF-7	breast:
2	chr5:59986799..59989085-chr5:59989251..59992450,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000035499	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10057004	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs10805370	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10939863	0.93[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs11741754	0.85[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs11750609	0.93[ASN][1000 genomes]
rs11955398	0.85[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs12517174	0.85[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs12517207	0.85[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs12655515	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13153359	0.93[CHB][hapmap]
rs13358053	0.92[CHB][hapmap]
rs1379116	0.84[CEU][hapmap]
rs17387940	0.85[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs2085412	0.83[ASN][1000 genomes]
rs4235480	0.81[ASN][1000 genomes]
rs4307050	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs4370226	0.91[ASN][1000 genomes]
rs4700385	0.81[ASN][1000 genomes]
rs56726435	0.82[EUR][1000 genomes]
rs57521726	1.00[ASN][1000 genomes]
rs6449483	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6449484	0.93[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs6449485	1.00[ASN][1000 genomes]
rs6449489	0.85[ASN][1000 genomes]
rs6874072	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs702564	0.92[CHB][hapmap]
rs7704338	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719726	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs897672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv462198	chr5:59969015-60116613	Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv598298	chr5:59969015-60116613	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1023403	chr5:59969534-60079822	Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv4850	chr5:59976186-60039810	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7719611	ELOVL7	cis	parietal	SCAN
rs7719611	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs7719611	ERCC8	Cis_1M	lymphoblastoid	RTeQTL
rs7719611	DEPDC1B	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59962600-59990000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:59966000-59988800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:59969600-59994800	Weak transcription	Fetal Lung	lung
4	chr5:59971000-59993800	Weak transcription	NHLF	lung
5	chr5:59971000-59994000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:59971000-59994200	Weak transcription	NH-A	brain
7	chr5:59974200-59994200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:59974400-59993600	Weak transcription	Hela-S3	cervix
9	chr5:59977200-59991000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:59977200-59991200	Weak transcription	Pancreas	Pancrea
11	chr5:59977200-59994800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:59980200-59995200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:59981800-59994200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr5:59982400-59993600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:59982600-59994800	Weak transcription	Fetal Muscle Leg	muscle
16	chr5:59982800-59991000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:59982800-59992400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:59982800-59993800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:59982800-59994800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr5:59982800-59994800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr5:59983000-59990000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:59983000-59990200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:59983000-59990800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:59983000-59991000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:59983000-59991000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:59983000-59991200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:59983000-59992800	Weak transcription	NHEK	skin
28	chr5:59983000-59994000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr5:59983000-59994000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr5:59983000-59994000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:59983000-59994200	Weak transcription	Thymus	Thymus
32	chr5:59983000-59994600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr5:59983000-59994800	Weak transcription	Fetal Thymus	thymus
34	chr5:59983000-59994800	Weak transcription	HSMM	muscle
35	chr5:59983200-59991000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:59983200-59993800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr5:59983200-59993800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:59983800-59991000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:59984200-59993000	Weak transcription	NHDF-Ad	bronchial
40	chr5:59984400-59991000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr5:59984400-59991200	Weak transcription	Dnd41	blood
42	chr5:59984600-59991000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr5:59984600-59991200	Weak transcription	A549	lung
44	chr5:59984600-59993000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:59984600-59994000	Weak transcription	Fetal Heart	heart
46	chr5:59984600-59994800	Weak transcription	Fetal Intestine Small	intestine
47	chr5:59985000-59991000	Weak transcription	K562	blood
48	chr5:59985200-59991200	Weak transcription	Placenta	Placenta
49	chr5:59986800-59992400	Weak transcription	HepG2	liver
50	chr5:59986800-59994000	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links