Variant report

Variant	rs1678991
Chromosome Location	chr15:42517791-42517792
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42517623..42519881-chr15:42564491..42566619,2	K562	blood:
2	chr15:42515383..42517801-chr15:42527177..42529552,2	K562	blood:
3	chr15:42513814..42516638-chr15:42517068..42519748,2	K562	blood:

Variant related genes	Relation type
ENSG00000103978	Chromatin interaction
ENSG00000214013	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10775126	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10851407	0.91[EUR][1000 genomes]
rs10851408	0.91[EUR][1000 genomes]
rs10851409	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11070370	0.87[EUR][1000 genomes]
rs11631917	0.91[EUR][1000 genomes]
rs11631983	0.90[EUR][1000 genomes]
rs11638784	0.81[EUR][1000 genomes]
rs12438562	0.84[EUR][1000 genomes]
rs12441642	0.96[EUR][1000 genomes]
rs12441700	0.82[EUR][1000 genomes]
rs12594162	0.91[EUR][1000 genomes]
rs12917101	0.91[EUR][1000 genomes]
rs1359003	0.82[EUR][1000 genomes]
rs1359004	0.82[EUR][1000 genomes]
rs1619030	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1659217	0.84[EUR][1000 genomes]
rs1678985	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678986	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679002	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1679009	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1679010	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1679012	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1703750	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1703755	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1712418	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1712421	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138831	0.96[EUR][1000 genomes]
rs2289295	0.84[EUR][1000 genomes]
rs2412682	0.91[EUR][1000 genomes]
rs2412685	0.91[EUR][1000 genomes]
rs2412705	0.84[EUR][1000 genomes]
rs2918459	0.84[EUR][1000 genomes]
rs2918461	0.84[EUR][1000 genomes]
rs3743006	0.84[EUR][1000 genomes]
rs3850774	0.82[EUR][1000 genomes]
rs4329897	0.84[EUR][1000 genomes]
rs4923940	0.87[EUR][1000 genomes]
rs4923943	0.87[EUR][1000 genomes]
rs4924645	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4924648	0.91[EUR][1000 genomes]
rs4924653	0.83[EUR][1000 genomes]
rs4924658	0.87[EUR][1000 genomes]
rs4924660	0.87[EUR][1000 genomes]
rs58313689	0.90[EUR][1000 genomes]
rs59132828	0.84[EUR][1000 genomes]
rs598360	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs622442	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs633934	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6493027	0.91[EUR][1000 genomes]
rs660126	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs677878	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7086	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7175863	0.84[EUR][1000 genomes]
rs7177120	0.83[EUR][1000 genomes]
rs7181742	0.84[EUR][1000 genomes]
rs7183015	0.84[EUR][1000 genomes]
rs7183546	0.84[EUR][1000 genomes]
rs73400993	0.82[EUR][1000 genomes]
rs765830	0.84[EUR][1000 genomes]
rs8024732	0.91[EUR][1000 genomes]
rs8025601	0.85[EUR][1000 genomes]
rs8031315	0.87[EUR][1000 genomes]
rs8033080	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8036046	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8036187	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8036380	0.84[EUR][1000 genomes]
rs8036596	0.87[EUR][1000 genomes]
rs8037020	0.91[EUR][1000 genomes]
rs9672382	0.96[EUR][1000 genomes]
rs9920921	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS 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	12 gene(s)	inside rSNPs	diseases
6	nsv1054102	chr15:42493052-42528765	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42500800-42563200	Weak transcription	Stomach Mucosa	stomach
2	chr15:42501000-42518600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:42501000-42518800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:42501000-42520800	Weak transcription	Psoas Muscle	Psoas
5	chr15:42501000-42534800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:42501000-42536600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:42501000-42536800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:42501000-42538000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:42501200-42523200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:42501200-42532400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr15:42501800-42536800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:42502000-42521200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:42502000-42535000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:42502200-42534000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:42502200-42536600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr15:42502400-42519600	Strong transcription	Fetal Intestine Large	intestine
17	chr15:42502800-42535200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:42502800-42536400	Strong transcription	Fetal Muscle Leg	muscle
19	chr15:42503200-42544000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:42504000-42517800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:42506800-42532000	Strong transcription	Placenta	Placenta
22	chr15:42508000-42532200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:42508200-42520400	Strong transcription	Fetal Thymus	thymus
24	chr15:42508200-42525000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:42509400-42535200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:42510800-42520200	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:42511800-42519000	Weak transcription	Fetal Heart	heart
28	chr15:42511800-42536800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr15:42512400-42518000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr15:42512400-42518400	Weak transcription	GM12878-XiMat	blood
31	chr15:42512800-42518200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:42513000-42519200	Strong transcription	Fetal Stomach	stomach
33	chr15:42513200-42523600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:42513200-42532200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:42513600-42520000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:42513800-42520000	Strong transcription	Thymus	Thymus
37	chr15:42513800-42534800	Strong transcription	Liver	Liver
38	chr15:42514000-42523600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:42514000-42526600	Strong transcription	Left Ventricle	heart
40	chr15:42514000-42534800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:42514000-42535200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:42514200-42519200	Strong transcription	Right Ventricle	heart
43	chr15:42514200-42520600	Strong transcription	Fetal Brain Female	brain
44	chr15:42514200-42521600	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr15:42514200-42522600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:42514200-42523400	Strong transcription	Duodenum Mucosa	Duodenum
47	chr15:42514200-42524200	Strong transcription	Stomach Smooth Muscle	stomach
48	chr15:42514200-42526600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr15:42514200-42527000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr15:42514200-42532400	Strong transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links