Variant report

Variant	rs157789
Chromosome Location	chr15:76805703-76805704
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76803456..76806308-chr15:77131835..77134067,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs157757	0.87[CEU][hapmap]
rs157760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs157761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs157762	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs157763	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs157766	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs157768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157769	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157775	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs157777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs157778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs157779	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs157788	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166906	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs166933	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16968196	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs172244	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1810348	0.87[CEU][hapmap];0.89[CHB][hapmap]
rs182253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1875883	0.83[EUR][1000 genomes]
rs190771	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2078437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2439984	0.87[CEU][hapmap];0.92[YRI][hapmap]
rs2439992	0.87[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs2460161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2468113	0.90[AFR][1000 genomes]
rs2468116	0.89[AFR][1000 genomes]
rs2468122	0.87[CEU][hapmap]
rs2468123	0.92[YRI][hapmap]
rs2468129	0.91[AFR][1000 genomes]
rs2469215	0.85[CEU][hapmap]
rs2469224	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2469241	0.87[AFR][1000 genomes]
rs2469554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2469556	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2585730	0.87[CEU][hapmap]
rs280001	0.87[CEU][hapmap]
rs280012	0.92[YRI][hapmap]
rs280013	0.87[CEU][hapmap]
rs283796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs283799	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs283802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284884	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs284885	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs284893	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs284897	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs284898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs284901	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs284902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs284903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs284904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs284905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs284907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2930681	0.87[CEU][hapmap];0.92[YRI][hapmap]
rs2938695	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2944377	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2948703	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2956873	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2957560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2957607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2957611	0.85[EUR][1000 genomes]
rs2957612	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2957613	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs387321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs403656	1.00[JPT][hapmap]
rs480672	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4886490	0.86[CEU][hapmap];0.89[CHB][hapmap]
rs4886491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4886492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs494268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8031672	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs874224	0.87[CEU][hapmap];0.89[CHB][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	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1053924	chr15:76803849-77089079	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs157789	ISL2	cis	Whole Blood	GTEx
rs157789	RP11-685G9.2	cis	Whole Blood	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76725800-76812600	Weak transcription	Left Ventricle	heart
2	chr15:76788400-76813600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr15:76791200-76806200	Weak transcription	Fetal Muscle Leg	muscle
4	chr15:76794000-76810400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:76794200-76806400	Weak transcription	Gastric	stomach
6	chr15:76795200-76806800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:76795800-76810600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:76796800-76806400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:76797000-76806400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:76797200-76806400	Weak transcription	Liver	Liver
11	chr15:76797400-76825000	Weak transcription	Primary B cells from cord blood	blood
12	chr15:76800400-76806000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr15:76804800-76808400	Enhancers	Fetal Intestine Small	intestine
14	chr15:76805000-76810200	Weak transcription	Fetal Heart	heart
15	chr15:76805200-76808400	Enhancers	Fetal Intestine Large	intestine
16	chr15:76805400-76806000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:76805400-76810400	Weak transcription	Fetal Stomach	stomach
18	chr15:76805600-76805800	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr15:76805600-76806400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:76805600-76807200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:76805600-76808400	Enhancers	HepG2	liver
22	chr15:76805600-76845800	Weak transcription	Primary T cells from cord blood	blood

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