Variant report

Variant	rs3743242
Chromosome Location	chr15:99669628-99669629
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:99669059..99671462-chr15:99672419..99674056,2	K562	blood:
2	chr15:99666915..99668960-chr15:99669184..99670795,2	MCF-7	breast:
3	chr15:99663432..99665582-chr15:99669095..99671723,2	MCF-7	breast:
4	chr15:99667943..99671738-chr15:99674113..99676768,3	K562	blood:
5	chr15:99667943..99670648-chr15:99673472..99676768,3	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11247059	0.81[ASN][1000 genomes]
rs11247071	0.83[CHB][hapmap]
rs11247076	0.82[CHB][hapmap]
rs11247077	0.84[CHB][hapmap]
rs11247078	0.84[CHB][hapmap]
rs11634417	0.87[ASN][1000 genomes]
rs12439693	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs12439819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs12439820	0.83[CHB][hapmap]
rs12440477	0.83[CEU][hapmap];0.94[CHB][hapmap]
rs12440640	0.91[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12440982	0.83[CEU][hapmap];0.94[CHB][hapmap]
rs12441965	0.83[CHB][hapmap]
rs12441996	0.83[CHB][hapmap]
rs12442235	0.91[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12593076	0.83[CHB][hapmap]
rs12594250	0.84[CHB][hapmap]
rs12594607	0.83[CHB][hapmap]
rs12595099	0.84[CHB][hapmap]
rs12901547	0.83[CHB][hapmap]
rs12902590	0.84[CHB][hapmap]
rs12906323	0.88[CHB][hapmap]
rs12906924	0.83[CHB][hapmap]
rs12907938	0.83[CHB][hapmap]
rs12914665	0.83[CHB][hapmap]
rs1612365	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1670229	0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1876741	0.91[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2006670	0.91[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2048303	0.83[CHB][hapmap]
rs2089708	0.83[CHB][hapmap]
rs2290352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2861371	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3134586	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3134587	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3134588	0.84[JPT][hapmap]
rs3759903	0.83[CHB][hapmap]
rs3961782	0.84[CHB][hapmap]
rs4965215	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4965216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4965443	0.90[ASN][1000 genomes]
rs4965446	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4965448	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4965451	0.91[CEU][hapmap];0.94[CHB][hapmap]
rs58319155	0.94[ASN][1000 genomes]
rs58627039	0.82[ASN][1000 genomes]
rs58653169	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60513984	0.92[EUR][1000 genomes]
rs7163435	0.83[CHB][hapmap]
rs7169355	0.83[CHB][hapmap]
rs7170952	0.83[CHB][hapmap]
rs7178606	0.83[CHB][hapmap]
rs73476394	0.87[ASN][1000 genomes]
rs73480175	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73480191	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8040268	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv533375	chr15:99443534-99696221	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv530685	chr15:99452377-99713365	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
16	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 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	chr15:99647600-99672400	Weak transcription	Esophagus	oesophagus
2	chr15:99652000-99669800	Weak transcription	Thymus	Thymus
3	chr15:99660600-99671600	Weak transcription	Liver	Liver
4	chr15:99663600-99679400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:99664200-99675800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:99664400-99678800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr15:99664400-99678800	Weak transcription	Brain Germinal Matrix	brain
8	chr15:99664600-99672600	Weak transcription	Small Intestine	intestine
9	chr15:99664600-99676800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:99664600-99677200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:99664600-99678800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:99664600-99682200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:99664800-99672800	Weak transcription	Fetal Thymus	thymus
14	chr15:99664800-99682000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr15:99664800-99688600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr15:99665000-99670000	Weak transcription	Colonic Mucosa	Colon
17	chr15:99665000-99670200	Weak transcription	HepG2	liver
18	chr15:99665000-99676000	Genic enhancers	Colon Smooth Muscle	Colon
19	chr15:99665000-99676600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:99665000-99676800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr15:99665000-99683800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr15:99665000-99714200	Weak transcription	NHEK	skin
23	chr15:99665200-99670000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:99665200-99676000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:99665200-99677400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr15:99665200-99677400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr15:99665200-99677600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:99665200-99679400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr15:99665200-99687800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:99665600-99670000	Weak transcription	Gastric	stomach
31	chr15:99665800-99670000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:99665800-99670200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:99665800-99670800	Weak transcription	Lung	lung
34	chr15:99665800-99670800	Weak transcription	NHLF	lung
35	chr15:99665800-99671000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:99665800-99671800	Strong transcription	Fetal Stomach	stomach
37	chr15:99665800-99676600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:99665800-99676800	Weak transcription	Ovary	ovary
39	chr15:99665800-99676800	Weak transcription	Spleen	Spleen
40	chr15:99665800-99677200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:99666000-99670200	Weak transcription	Brain Angular Gyrus	brain
42	chr15:99666000-99671600	Strong transcription	A549	lung
43	chr15:99666000-99675200	Weak transcription	HSMM	muscle
44	chr15:99666000-99675400	Weak transcription	Osteobl	bone
45	chr15:99666000-99683000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:99666200-99669800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr15:99666200-99675400	Weak transcription	NHDF-Ad	bronchial
48	chr15:99666200-99680400	Weak transcription	Fetal Brain Female	brain
49	chr15:99666200-99684200	Weak transcription	HSMMtube	muscle
50	chr15:99666400-99679800	Genic enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links