Variant report

Variant	rs10495953
Chromosome Location	chr2:48811854-48811855
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	chr2:48806857..48808745-chr2:48811544..48813174,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068781	Chromatin interaction
ENSG00000243244	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs11125176	0.84[EUR][1000 genomes]
rs11676150	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11678306	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11680574	0.93[CEU][hapmap];0.96[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11681276	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11681426	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11683611	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11693429	0.89[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11693559	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693691	0.93[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12475789	0.97[ASN][1000 genomes]
rs12990079	1.00[CHB][hapmap];0.96[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12992755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12992870	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12999304	0.87[EUR][1000 genomes]
rs13010692	0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13011288	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs13014112	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13016899	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13025488	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13027618	0.89[CEU][hapmap];0.96[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13030948	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13031184	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13034063	0.81[EUR][1000 genomes]
rs13034951	0.89[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17037412	0.96[CHB][hapmap]
rs17039250	0.93[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1996970	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2103112	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2177489	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2293270	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2293271	0.80[ASN][1000 genomes]
rs2293272	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2293274	0.86[EUR][1000 genomes]
rs2349098	0.88[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2882084	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3749142	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3749144	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3749145	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792234	0.87[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3792235	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792236	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792237	0.93[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792238	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3828340	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4566410	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953593	0.84[EUR][1000 genomes]
rs55641971	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55700200	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55858189	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56111874	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62135201	0.80[EUR][1000 genomes]
rs62135230	0.92[ASN][1000 genomes]
rs62135231	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62135232	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62135233	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62135236	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545048	0.89[ASN][1000 genomes]
rs66888174	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6709043	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6710565	0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs6712592	0.93[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6712724	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6716291	1.00[CHB][hapmap];0.96[JPT][hapmap];0.93[YRI][hapmap];0.97[ASN][1000 genomes]
rs6722556	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6727929	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6732365	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6737732	0.85[EUR][1000 genomes]
rs6741341	0.93[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6741677	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6742725	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6757847	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6761796	0.99[ASN][1000 genomes]
rs940389	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv581776	chr2:48763382-48913019	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking 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	10 gene(s)	inside rSNPs	diseases
8	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10495953	STON1	cis	Esophagus Muscularis	GTEx
rs10495953	STON1-GTF2A1L	cis	lung	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48759000-48827600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr2:48788600-48812000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:48794400-48812000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:48794400-48827200	Weak transcription	NHDF-Ad	bronchial
5	chr2:48795400-48812000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:48795400-48814200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:48795600-48826000	Weak transcription	Fetal Intestine Small	intestine
8	chr2:48798800-48815600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:48799000-48825800	Weak transcription	HSMMtube	muscle
10	chr2:48800000-48812000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:48800400-48812600	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:48800400-48813400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:48800400-48814000	Weak transcription	Lung	lung
14	chr2:48800800-48812800	Weak transcription	Brain Germinal Matrix	brain
15	chr2:48803400-48812000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:48804600-48824600	Weak transcription	Fetal Intestine Large	intestine
17	chr2:48804800-48816200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:48807600-48813600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:48807800-48812800	Strong transcription	Stomach Smooth Muscle	stomach
20	chr2:48807800-48814200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:48807800-48815200	Strong transcription	Fetal Stomach	stomach
22	chr2:48807800-48815400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:48808000-48813000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:48808200-48812000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:48808400-48827600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:48808600-48814000	Weak transcription	Psoas Muscle	Psoas
27	chr2:48808600-48821200	Weak transcription	Fetal Kidney	kidney
28	chr2:48808600-48834800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:48808800-48821000	Weak transcription	Adipose Nuclei	Adipose
30	chr2:48809000-48821000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:48809000-48824400	Weak transcription	Left Ventricle	heart
32	chr2:48809600-48812200	Weak transcription	Brain Substantia Nigra	brain
33	chr2:48809600-48813400	Weak transcription	Fetal Lung	lung
34	chr2:48809600-48814000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr2:48809600-48814600	Weak transcription	Ovary	ovary
36	chr2:48809600-48821000	Weak transcription	Aorta	Aorta
37	chr2:48809600-48827200	Weak transcription	Right Ventricle	heart
38	chr2:48809800-48812200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:48809800-48828600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:48810200-48812400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:48810400-48812000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:48810600-48812200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:48810600-48812800	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:48810800-48816400	Enhancers	Placenta	Placenta
45	chr2:48811200-48812200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:48811600-48816400	Enhancers	Placenta Amnion	Placenta Amnion
47	chr2:48811800-48812200	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr2:48811800-48812400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:48811800-48813400	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr2:48811800-48813800	Genic enhancers	Fetal Muscle Leg	muscle

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