Variant report

Variant	rs4722999
Chromosome Location	chr7:30693775-30693776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:30692169..30694201-chr7:30696572..30698113,2	MCF-7	breast:
2	chr7:30687553..30692507-chr7:30692949..30698507,6	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs10227133	0.81[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs10232372	0.86[ASN][1000 genomes]
rs10239660	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10243040	0.86[ASN][1000 genomes]
rs10249885	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10265589	0.82[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10480088	0.86[ASN][1000 genomes]
rs1074373	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1141114	0.86[ASN][1000 genomes]
rs11761080	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12532057	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12533961	0.82[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs13228758	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1468402	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1558064	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16875282	0.85[ASN][1000 genomes]
rs16875285	0.86[ASN][1000 genomes]
rs2009662	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2214837	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2240401	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2267710	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2270025	0.82[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2391870	0.83[GIH][hapmap]
rs3779250	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3807632	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4722992	0.85[ASN][1000 genomes]
rs6462211	0.84[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6947982	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6970688	0.86[ASN][1000 genomes]
rs6970807	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs929377	0.84[CHD][hapmap];0.84[GIH][hapmap]
rs9648369	0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[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	nsv538811	chr7:30549595-31405593	Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1016256	chr7:30649212-31163056	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1023120	chr7:30655070-31185096	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv2761316	chr7:30655082-31166676	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv527038	chr7:30657467-31161945	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv916877	chr7:30661135-31154731	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1017168	chr7:30663213-31166676	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv1017808	chr7:30671936-31150473	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv830938	chr7:30684230-30897523	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4722999	AC005154.6	cis	Esophagus Muscularis	GTEx
rs4722999	AC005154.6	cis	Artery Aorta	GTEx
rs4722999	AC005154.6	cis	Stomach	GTEx
rs4722999	AC005154.6	cis	lung	GTEx
rs4722999	AC005154.6	cis	Esophagus Mucosa	GTEx
rs4722999	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs4722999	AC005154.6	cis	Artery Tibial	GTEx
rs4722999	CREB5	cis	cerebellum	SCAN
rs4722999	AC005154.6	cis	Nerve Tibial	GTEx
rs4722999	FKBP9	cis	parietal	SCAN
rs4722999	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs4722999	CRHR2	cis	parietal	SCAN
rs4722999	AC005154.6	cis	Thyroid	GTEx
rs4722999	LOC401320	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30674200-30699600	Weak transcription	Fetal Brain Male	brain
2	chr7:30675600-30696200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:30675600-30698800	Weak transcription	Ovary	ovary
4	chr7:30675800-30693800	Weak transcription	Spleen	Spleen
5	chr7:30675800-30695200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr7:30675800-30695600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr7:30676000-30698800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr7:30676000-30700400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:30682800-30696000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr7:30683400-30695200	Weak transcription	Fetal Intestine Large	intestine
11	chr7:30684000-30697000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr7:30684200-30699800	Weak transcription	Brain Germinal Matrix	brain
13	chr7:30685200-30694000	Weak transcription	Fetal Intestine Small	intestine
14	chr7:30685200-30694000	Weak transcription	Pancreas	Pancrea
15	chr7:30686000-30693800	Weak transcription	Fetal Muscle Leg	muscle
16	chr7:30686000-30698800	Weak transcription	Lung	lung
17	chr7:30686200-30696000	Weak transcription	Brain Hippocampus Middle	brain
18	chr7:30686200-30703200	Weak transcription	Esophagus	oesophagus
19	chr7:30686600-30699800	Weak transcription	Gastric	stomach
20	chr7:30686800-30694000	Weak transcription	Fetal Stomach	stomach
21	chr7:30687000-30696600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:30687200-30695200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr7:30687200-30698600	Weak transcription	NHEK	skin
24	chr7:30687400-30695800	Weak transcription	Primary T cells from cord blood	blood
25	chr7:30687800-30695000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:30688400-30699600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr7:30688800-30706400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr7:30690200-30704000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:30691400-30701600	Weak transcription	Right Atrium	heart
30	chr7:30691800-30696000	Strong transcription	Fetal Brain Female	brain
31	chr7:30691800-30697000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:30692400-30694000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr7:30692600-30694400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr7:30693600-30694400	Strong transcription	Skeletal Muscle Male	skeletal muscle

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