Variant report

Variant	rs1878940
Chromosome Location	chr15:73596823-73596824
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	chr15:73596786..73598480-chr15:73926127..73928459,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156642	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1017808	0.84[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs10518997	1.00[YRI][hapmap]
rs11072405	0.87[JPT][hapmap]
rs11072407	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11072408	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11072411	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072412	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1119251	0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11634045	0.83[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs11636981	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs11856537	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12439852	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440576	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12442755	0.83[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12591304	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12594776	0.84[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12901272	0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12901649	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs1382782	0.87[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs1564347	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1585766	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs16957683	0.84[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs1904335	0.80[ASN][1000 genomes]
rs2061890	0.82[ASN][1000 genomes]
rs2252725	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2292915	0.83[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2415145	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2415146	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2660821	0.90[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2680338	0.97[ASN][1000 genomes]
rs2680340	0.91[ASN][1000 genomes]
rs2680341	0.95[ASN][1000 genomes]
rs34456824	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34953385	0.80[ASN][1000 genomes]
rs35348961	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35391014	0.85[ASN][1000 genomes]
rs35608416	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35778649	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36072085	0.83[ASN][1000 genomes]
rs3743496	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3784795	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3859014	0.86[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3859015	0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs472681	0.91[ASN][1000 genomes]
rs4776631	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4777587	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs4777592	0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs486267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs489531	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs498005	0.81[CHB][hapmap]
rs520824	0.95[ASN][1000 genomes]
rs549253	0.96[ASN][1000 genomes]
rs559260	0.99[ASN][1000 genomes]
rs563076	0.99[ASN][1000 genomes]
rs564765	0.94[ASN][1000 genomes]
rs570001	0.87[ASN][1000 genomes]
rs576813	0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs59628124	0.82[ASN][1000 genomes]
rs62015498	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6495057	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs7177758	0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs72741448	0.83[ASN][1000 genomes]
rs7495084	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs8039418	0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73536200-73602000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:73552800-73598400	Weak transcription	Small Intestine	intestine
3	chr15:73560800-73597200	Strong transcription	Rectal Mucosa Donor 31	rectum
4	chr15:73563200-73598600	Weak transcription	Stomach Mucosa	stomach
5	chr15:73566400-73597800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:73568600-73600800	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr15:73570200-73597000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:73570400-73597000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:73571200-73601400	Strong transcription	Fetal Stomach	stomach
10	chr15:73577800-73598200	Strong transcription	Duodenum Mucosa	Duodenum
11	chr15:73579200-73598200	Weak transcription	Psoas Muscle	Psoas
12	chr15:73581600-73598000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:73582000-73598000	Weak transcription	Fetal Heart	heart
14	chr15:73583400-73597000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr15:73583400-73598400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:73584600-73598000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:73584800-73597000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:73585000-73599400	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr15:73585400-73597200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr15:73585400-73599600	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:73585600-73597000	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr15:73586800-73601200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:73587200-73597000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:73587200-73597000	Strong transcription	Brain Angular Gyrus	brain
25	chr15:73587600-73597400	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:73588400-73598000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr15:73588600-73598200	Weak transcription	Hela-S3	cervix
28	chr15:73588600-73598600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:73588800-73597800	Weak transcription	HMEC	breast
30	chr15:73588800-73601400	Strong transcription	Fetal Intestine Large	intestine
31	chr15:73588800-73601800	Strong transcription	Fetal Intestine Small	intestine
32	chr15:73589200-73597200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:73590000-73597000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:73591400-73597600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr15:73591400-73598200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr15:73591400-73598600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr15:73592600-73597800	Strong transcription	Brain Hippocampus Middle	brain
38	chr15:73593000-73598000	Strong transcription	Brain Germinal Matrix	brain
39	chr15:73593200-73597000	Strong transcription	Fetal Brain Female	brain
40	chr15:73593200-73597000	Strong transcription	Ovary	ovary
41	chr15:73593200-73597000	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:73593200-73598000	Strong transcription	Brain Cingulate Gyrus	brain
43	chr15:73593200-73601800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:73593200-73602000	Strong transcription	Aorta	Aorta
45	chr15:73593400-73597200	Strong transcription	Gastric	stomach
46	chr15:73593400-73598600	Weak transcription	A549	lung
47	chr15:73593600-73597000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:73593600-73597000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:73594200-73598200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr15:73595000-73597800	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links