Variant report

Variant	rs971757
Chromosome Location	chr15:74487846-74487847
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74481853..74488513-chr15:74489689..74497281,13	MCF-7	breast:
2	chr15:74483505..74486452-chr15:74486727..74489080,2	MCF-7	breast:
3	chr15:74473602..74475447-chr15:74485969..74488494,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-247C2.2.1-6	chr15:74487672-74488016	NONHSAT047214

Variant related genes	Relation type
ENSG00000137868	Chromatin interaction
ENSG00000259264	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11630317	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs11630924	0.91[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11631509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11631944	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs11633687	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11639090	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11639369	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11854957	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs11857410	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12899173	0.82[CEU][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12905521	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12907503	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12911581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12912258	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12912578	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs12913041	0.90[EUR][1000 genomes]
rs12915891	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13259	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs2062309	0.87[EUR][1000 genomes]
rs2415169	0.88[EUR][1000 genomes]
rs2899824	0.82[CEU][hapmap];0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34004794	0.81[AMR][1000 genomes]
rs34147822	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34234753	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34573746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34591452	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34868798	0.88[EUR][1000 genomes]
rs34985083	0.81[AMR][1000 genomes]
rs35036456	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35255788	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35462746	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35661273	0.88[EUR][1000 genomes]
rs35917667	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3848160	0.89[EUR][1000 genomes]
rs3848161	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs3888004	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs409856	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs62003660	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62003661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62005707	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62005709	0.89[EUR][1000 genomes]
rs62005710	0.89[EUR][1000 genomes]
rs62005711	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71399778	0.89[EUR][1000 genomes]
rs72747610	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs733163	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8037531	0.88[EUR][1000 genomes]
rs923118	0.88[EUR][1000 genomes]
rs9630417	0.87[EUR][1000 genomes]
rs971755	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs971756	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1050884	chr15:74394983-74489413	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv904345	chr15:74458181-74526596	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv904347	chr15:74462629-74537101	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv904348	chr15:74462629-74542686	Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74466200-74492800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:74469200-74491800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr15:74469400-74493200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:74470800-74492800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:74473600-74488200	Weak transcription	Right Atrium	heart
6	chr15:74478600-74491400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:74480600-74491800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:74481000-74488400	Weak transcription	Right Ventricle	heart
9	chr15:74482800-74488000	Strong transcription	Fetal Stomach	stomach
10	chr15:74483800-74488200	Enhancers	Hela-S3	cervix
11	chr15:74484000-74490000	Enhancers	HSMM	muscle
12	chr15:74484800-74488800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr15:74485000-74488200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:74485000-74489800	Enhancers	NH-A	brain
15	chr15:74485200-74488000	Genic enhancers	A549	lung
16	chr15:74485400-74493000	Weak transcription	Fetal Thymus	thymus
17	chr15:74485800-74491000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:74485800-74492600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:74486000-74488400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:74486000-74490200	Enhancers	Esophagus	oesophagus
21	chr15:74486200-74488000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr15:74486400-74488400	Weak transcription	NHDF-Ad	bronchial
23	chr15:74486400-74491400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:74486600-74488000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:74486600-74488400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:74486600-74488400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:74486800-74488000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:74486800-74488200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:74486800-74488400	Weak transcription	HMEC	breast
30	chr15:74486800-74488600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr15:74486800-74488600	Weak transcription	NHLF	lung
32	chr15:74487000-74488200	Weak transcription	Osteobl	bone
33	chr15:74487000-74488400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:74487000-74488600	Weak transcription	NHEK	skin
35	chr15:74487200-74488200	Strong transcription	Fetal Intestine Small	intestine
36	chr15:74487200-74488800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr15:74487400-74488400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:74487400-74489600	Enhancers	Spleen	Spleen
39	chr15:74487400-74490200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:74487400-74491600	Genic enhancers	Placenta	Placenta
41	chr15:74487600-74488000	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr15:74487600-74488000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:74487600-74489400	Enhancers	Lung	lung
44	chr15:74487600-74489600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:74487600-74489600	Enhancers	Fetal Muscle Leg	muscle
46	chr15:74487600-74489800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:74487600-74489800	Enhancers	Fetal Heart	heart
48	chr15:74487600-74492600	Weak transcription	GM12878-XiMat	blood
49	chr15:74487800-74488000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr15:74487800-74489400	Enhancers	Fetal Lung	lung

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