Variant report

Variant	rs1560474
Chromosome Location	chr18:6861173-6861174
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10775437	1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11081279	0.81[JPT][hapmap];0.98[ASN][1000 genomes]
rs1241989	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12604439	0.87[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12608382	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1431386	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2163465	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2567261	0.87[CEU][hapmap];0.87[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4536541	0.98[ASN][1000 genomes]
rs67003835	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs67162636	0.97[ASN][1000 genomes]
rs67382010	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7232013	0.99[ASN][1000 genomes]
rs7233874	0.99[ASN][1000 genomes]
rs7238947	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7243173	0.87[JPT][hapmap];0.99[ASN][1000 genomes]
rs8082943	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916883	chr18:6299209-7244642	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1063762	chr18:6542534-7382339	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv543630	chr18:6542534-7382339	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers 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	39 gene(s)	inside rSNPs	diseases
4	nsv1060757	chr18:6682974-7051982	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv543631	chr18:6682974-7051982	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1064175	chr18:6740267-7384528	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv576397	chr18:6758921-7036683	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
8	esv2758469	chr18:6762909-6943645	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	esv2758711	chr18:6762909-6943645	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1059956	chr18:6786579-7382339	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv543632	chr18:6786579-7382339	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	nsv1060826	chr18:6846443-6983289	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv1059970	chr18:6846443-7281397	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
14	nsv543633	chr18:6846443-7281397	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
15	nsv1064956	chr18:6846503-7281337	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
16	nsv543634	chr18:6846503-7281337	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
17	nsv1061855	chr18:6846738-6868487	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:6850400-6861400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr18:6852200-6874400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr18:6853200-6870400	Weak transcription	Placenta	Placenta
4	chr18:6853400-6868000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr18:6854000-6875200	Weak transcription	Fetal Kidney	kidney
6	chr18:6855200-6862400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr18:6855600-6871200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr18:6855600-6895200	Weak transcription	Pancreas	Pancrea
9	chr18:6855800-6871200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr18:6856000-6870200	Weak transcription	HSMM	muscle
11	chr18:6856000-6871000	Weak transcription	Lung	lung
12	chr18:6856000-6877200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr18:6856000-6887000	Weak transcription	Fetal Intestine Large	intestine
14	chr18:6856000-6887000	Weak transcription	Fetal Intestine Small	intestine
15	chr18:6856200-6877400	Weak transcription	Spleen	Spleen
16	chr18:6857600-6871600	Weak transcription	Fetal Brain Male	brain
17	chr18:6858400-6862400	Strong transcription	Fetal Muscle Leg	muscle
18	chr18:6858600-6877400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr18:6859200-6861800	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr18:6859200-6862200	Strong transcription	Fetal Lung	lung
21	chr18:6859200-6862400	Strong transcription	Fetal Stomach	stomach
22	chr18:6859200-6862400	Strong transcription	Ovary	ovary
23	chr18:6859600-6861200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr18:6859600-6861600	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr18:6859800-6861600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr18:6859800-6862600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr18:6860200-6861800	Enhancers	H9 Cell Line	embryonic stem cell
28	chr18:6860200-6861800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr18:6860400-6861400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr18:6860400-6861400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr18:6860400-6861400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr18:6860400-6861600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr18:6860400-6861600	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr18:6860400-6861600	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr18:6860400-6861800	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr18:6860400-6861800	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr18:6860400-6862000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr18:6860600-6861200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr18:6860600-6861800	Enhancers	H1 Cell Line	embryonic stem cell
40	chr18:6860600-6862000	Strong transcription	Adipose Nuclei	Adipose
41	chr18:6860600-6862200	Strong transcription	HSMMtube	muscle
42	chr18:6860600-6862400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr18:6860600-6863400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr18:6860800-6861800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr18:6860800-6871400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr18:6861000-6861200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr18:6861000-6861400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr18:6861000-6861800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr18:6861000-6862400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links