Variant report

Variant	rs1648860
Chromosome Location	chr15:42224676-42224677
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42219188..42222413-chr15:42224091..42227939,3	MCF-7	breast:
2	chr15:42217980..42220140-chr15:42223299..42225570,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1197675	1.00[CHB][hapmap]
rs1648858	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648859	1.00[CEU][hapmap];1.00[CHB][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]
rs1704402	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1704404	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17687461	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17687821	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17687870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55971229	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73410628	0.81[AFR][1000 genomes]
rs8041703	1.00[CHB][hapmap]
rs890503	1.00[CHB][hapmap]

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	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv904116	chr15:42076387-42229852	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
5	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
6	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
7	nsv1054728	chr15:42177772-42310009	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42201200-42225400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:42202200-42225200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:42210600-42225400	Weak transcription	K562	blood
4	chr15:42210800-42230400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:42211600-42226200	Weak transcription	Thymus	Thymus
6	chr15:42212000-42225400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:42217800-42225400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:42217800-42225400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr15:42219000-42225200	Weak transcription	Fetal Thymus	thymus
10	chr15:42219400-42225600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:42219400-42226000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr15:42219400-42226600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr15:42219800-42225200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:42219800-42225400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr15:42219800-42225600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:42220000-42226600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:42220400-42224800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:42220600-42225400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr15:42220800-42227400	Enhancers	Placenta	Placenta
20	chr15:42220800-42230000	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr15:42221200-42225400	Weak transcription	Spleen	Spleen
22	chr15:42221200-42228600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:42221400-42225200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:42221400-42225800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr15:42221400-42226400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr15:42221600-42225000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr15:42221600-42225000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:42221600-42225200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:42221600-42229400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:42221600-42232400	Weak transcription	Ovary	ovary
31	chr15:42221800-42225000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr15:42221800-42225400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr15:42221800-42225400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr15:42221800-42225400	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr15:42221800-42225800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr15:42221800-42226200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:42221800-42230800	Enhancers	Adipose Nuclei	Adipose
38	chr15:42221800-42236400	Weak transcription	Brain Angular Gyrus	brain
39	chr15:42222000-42228000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr15:42222200-42225200	Weak transcription	Gastric	stomach
41	chr15:42222200-42249800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr15:42222400-42225600	Genic enhancers	NHEK	skin
43	chr15:42222800-42227800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:42222800-42235200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:42222800-42237600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr15:42223000-42224800	Weak transcription	Fetal Lung	lung
47	chr15:42223000-42225200	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr15:42223000-42225400	Weak transcription	Pancreas	Pancrea
49	chr15:42223000-42226400	Weak transcription	Small Intestine	intestine
50	chr15:42223000-42226400	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links