Variant report

Variant	rs1670229
Chromosome Location	chr15:99665697-99665698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:99664100..99665791-chr15:99675684..99677549,2	MCF-7	breast:
2	chr15:99644993..99646793-chr15:99665159..99667351,2	MCF-7	breast:
3	chr15:99664166..99665904-chr15:99695053..99697897,2	MCF-7	breast:
4	chr15:99658366..99661719-chr15:99663030..99668142,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182253	Chromatin interaction
ENSG00000259475	Chromatin interaction
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11247059	0.83[ASN][1000 genomes]
rs11247071	0.82[CHB][hapmap]
rs11247076	0.81[CHB][hapmap]
rs11247077	0.82[CHB][hapmap]
rs11247078	0.82[CHB][hapmap]
rs11634417	0.88[ASN][1000 genomes]
rs12437673	0.89[EUR][1000 genomes]
rs12439693	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs12439819	0.94[CHB][hapmap]
rs12439820	0.82[CHB][hapmap]
rs12440477	0.88[CHB][hapmap]
rs12440640	0.94[CHB][hapmap]
rs12440982	0.88[CHB][hapmap]
rs12441965	0.82[CHB][hapmap]
rs12441996	0.82[CHB][hapmap]
rs12442235	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs12593076	0.82[CHB][hapmap]
rs12594250	0.82[CHB][hapmap]
rs12594607	0.82[CHB][hapmap]
rs12595099	0.81[CHB][hapmap]
rs12901547	0.82[CHB][hapmap]
rs12902590	0.82[CHB][hapmap]
rs12906323	0.80[CHB][hapmap]
rs12906924	0.82[CHB][hapmap]
rs12907938	0.82[CHB][hapmap]
rs12914665	0.82[CHB][hapmap]
rs1612365	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1876741	0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs2006670	0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs2048228	0.92[EUR][1000 genomes]
rs2089708	0.82[CHB][hapmap]
rs2290352	0.94[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs2861371	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs3134586	0.96[ASN][1000 genomes]
rs3134587	0.96[ASN][1000 genomes]
rs3743242	0.95[ASN][1000 genomes]
rs3759903	0.82[CHB][hapmap]
rs3961782	0.82[CHB][hapmap]
rs4965215	0.83[ASN][1000 genomes]
rs4965216	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs4965443	0.91[ASN][1000 genomes]
rs4965446	0.94[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs4965448	0.86[ASN][1000 genomes]
rs4965451	0.88[CHB][hapmap]
rs58085631	0.89[EUR][1000 genomes]
rs58319155	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58627039	0.80[ASN][1000 genomes]
rs58653169	0.80[ASN][1000 genomes]
rs7163435	0.82[CHB][hapmap]
rs7169355	0.82[CHB][hapmap]
rs7170952	0.82[CHB][hapmap]
rs7178606	0.82[CHB][hapmap]
rs73476358	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73476394	0.88[ASN][1000 genomes]
rs73480175	0.80[ASN][1000 genomes]
rs73480191	0.80[ASN][1000 genomes]
rs7496161	0.82[CHB][hapmap]
rs8040268	0.86[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:100 , 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	chr15:99661000-99666400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:99662600-99666600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:99662800-99666200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr15:99663200-99666200	Flanking Active TSS	Hela-S3	cervix
8	chr15:99663200-99666400	Enhancers	Fetal Brain Male	brain
9	chr15:99663200-99666400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr15:99663200-99666800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:99663200-99666800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
12	chr15:99663400-99665800	Enhancers	Lung	lung
13	chr15:99663600-99665800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr15:99663600-99666000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:99663600-99667000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:99663600-99679400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr15:99664000-99666000	Flanking Active TSS	HSMMtube	muscle
18	chr15:99664000-99666200	Enhancers	Fetal Brain Female	brain
19	chr15:99664200-99665800	Enhancers	Spleen	Spleen
20	chr15:99664200-99666200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr15:99664200-99666800	Enhancers	Fetal Muscle Trunk	muscle
22	chr15:99664200-99667200	Enhancers	Fetal Muscle Leg	muscle
23	chr15:99664200-99675800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:99664400-99665800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:99664400-99665800	Genic enhancers	Fetal Stomach	stomach
26	chr15:99664400-99665800	Enhancers	Ovary	ovary
27	chr15:99664400-99666000	Enhancers	Brain Angular Gyrus	brain
28	chr15:99664400-99666000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr15:99664400-99666400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr15:99664400-99666800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:99664400-99666800	Enhancers	Brain Substantia Nigra	brain
32	chr15:99664400-99667200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:99664400-99667400	Enhancers	Right Atrium	heart
34	chr15:99664400-99678800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:99664400-99678800	Weak transcription	Brain Germinal Matrix	brain
36	chr15:99664600-99665800	Enhancers	Aorta	Aorta
37	chr15:99664600-99666200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
38	chr15:99664600-99666200	Enhancers	Brain Cingulate Gyrus	brain
39	chr15:99664600-99666200	Enhancers	HUVEC	blood vessel
40	chr15:99664600-99666200	Enhancers	NHDF-Ad	bronchial
41	chr15:99664600-99666600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:99664600-99666600	Enhancers	Brain Anterior Caudate	brain
43	chr15:99664600-99667200	Enhancers	Left Ventricle	heart
44	chr15:99664600-99667400	Enhancers	Psoas Muscle	Psoas
45	chr15:99664600-99668800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr15:99664600-99672600	Weak transcription	Small Intestine	intestine
47	chr15:99664600-99676800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr15:99664600-99677200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:99664600-99678800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr15:99664600-99682200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links