Variant report

Variant	rs68165049
Chromosome Location	chr20:25511676-25511677
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	chr20:25499922..25502486-chr20:25510143..25513350,3	MCF-7	breast:
2	chr20:25371156..25372734-chr20:25509417..25511739,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100997	Chromatin interaction

Extended variants
information (count: 165 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs10485776	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109100	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1122769	0.82[EUR][1000 genomes]
rs12106173	0.85[EUR][1000 genomes]
rs16987786	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16987789	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16987799	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16987820	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16988014	0.82[EUR][1000 genomes]
rs2179458	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2388026	0.85[EUR][1000 genomes]
rs242133	0.93[EUR][1000 genomes]
rs2424719	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35666277	0.94[ASN][1000 genomes]
rs3764695	0.85[EUR][1000 genomes]
rs400070	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs402120	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs409322	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs409401	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4098823	0.85[EUR][1000 genomes]
rs4098824	0.85[EUR][1000 genomes]
rs4113658	0.85[EUR][1000 genomes]
rs4113659	0.85[EUR][1000 genomes]
rs4113662	0.85[EUR][1000 genomes]
rs426563	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs428278	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4343537	0.85[EUR][1000 genomes]
rs440612	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs447808	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4574179	0.85[EUR][1000 genomes]
rs4813570	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57638633	0.85[EUR][1000 genomes]
rs58169034	0.85[EUR][1000 genomes]
rs58184048	0.94[ASN][1000 genomes]
rs58877578	0.82[ASN][1000 genomes]
rs59324912	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59546510	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037128	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6037131	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037133	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6037159	0.84[EUR][1000 genomes]
rs6037161	0.84[EUR][1000 genomes]
rs6037179	0.85[EUR][1000 genomes]
rs6037180	0.85[EUR][1000 genomes]
rs6037193	0.81[EUR][1000 genomes]
rs6037195	0.85[EUR][1000 genomes]
rs6037198	0.85[EUR][1000 genomes]
rs6037199	0.85[EUR][1000 genomes]
rs6037208	0.85[EUR][1000 genomes]
rs6037217	0.85[EUR][1000 genomes]
rs6037223	0.85[EUR][1000 genomes]
rs6050651	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6050658	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050663	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050692	0.84[EUR][1000 genomes]
rs6050709	0.82[EUR][1000 genomes]
rs6050710	0.82[EUR][1000 genomes]
rs6050712	0.84[EUR][1000 genomes]
rs6050714	0.84[EUR][1000 genomes]
rs6050717	0.84[EUR][1000 genomes]
rs6050758	0.85[EUR][1000 genomes]
rs6050763	0.85[EUR][1000 genomes]
rs6050765	0.85[EUR][1000 genomes]
rs6050768	0.80[EUR][1000 genomes]
rs6050775	0.85[EUR][1000 genomes]
rs6050787	0.85[EUR][1000 genomes]
rs6050788	0.85[EUR][1000 genomes]
rs6050789	0.85[EUR][1000 genomes]
rs6050793	0.85[EUR][1000 genomes]
rs6050795	0.85[EUR][1000 genomes]
rs6050799	0.85[EUR][1000 genomes]
rs6050802	0.85[EUR][1000 genomes]
rs6050804	0.85[EUR][1000 genomes]
rs6050807	0.85[EUR][1000 genomes]
rs6050809	0.85[EUR][1000 genomes]
rs6050815	0.85[EUR][1000 genomes]
rs6050832	0.80[EUR][1000 genomes]
rs6050834	0.85[EUR][1000 genomes]
rs6050838	0.85[EUR][1000 genomes]
rs6050841	0.85[EUR][1000 genomes]
rs6050846	0.85[EUR][1000 genomes]
rs6050847	0.85[EUR][1000 genomes]
rs6050848	0.85[EUR][1000 genomes]
rs6050851	0.85[EUR][1000 genomes]
rs6050853	0.85[EUR][1000 genomes]
rs6050854	0.85[EUR][1000 genomes]
rs6083886	0.86[EUR][1000 genomes]
rs66467007	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66591653	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66927803	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66940055	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67359112	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67455519	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67482703	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67679582	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67680401	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67921634	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68149491	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7260843	0.82[ASN][1000 genomes]
rs7261902	0.82[ASN][1000 genomes]
rs7266130	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7266592	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7274550	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73337339	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73337343	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73337346	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73337349	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73337355	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73337356	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73337364	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73337366	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73337369	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73337372	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73337394	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73337401	0.82[ASN][1000 genomes]
rs73339323	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73339335	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73339379	0.82[EUR][1000 genomes]
rs73341361	0.85[EUR][1000 genomes]
rs73341397	0.81[EUR][1000 genomes]
rs73343217	0.85[EUR][1000 genomes]
rs73343255	0.85[EUR][1000 genomes]
rs73345232	0.85[EUR][1000 genomes]
rs73345259	0.85[EUR][1000 genomes]
rs73345280	0.82[EUR][1000 genomes]
rs73597810	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73597811	1.00[ASN][1000 genomes]
rs73597812	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73597813	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742435	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742436	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8115484	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8115742	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8116267	0.82[EUR][1000 genomes]
rs8116474	0.87[EUR][1000 genomes]
rs8117181	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8117253	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8120594	0.84[EUR][1000 genomes]
rs8120972	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8121648	0.85[EUR][1000 genomes]
rs8122516	0.87[EUR][1000 genomes]
rs8122589	0.82[EUR][1000 genomes]
rs8126111	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs926487	0.85[EUR][1000 genomes]
rs9753575	0.85[EUR][1000 genomes]
rs981440	0.85[EUR][1000 genomes]
rs981441	0.85[EUR][1000 genomes]
rs9941769	0.85[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	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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 target site	24 gene(s)	inside rSNPs	diseases
2	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers 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	23 gene(s)	inside rSNPs	diseases
4	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1062765	chr20:25466482-25556751	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv544225	chr20:25466482-25556751	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv2762069	chr20:25506582-25619528	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	nsv979406	chr20:25509600-25513942	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs68165049	ZNF337	cis	lung	GTEx
rs68165049	RP4-694B14.5	cis	lung	GTEx
rs68165049	ZNF337	cis	Stomach	GTEx
rs68165049	RP4-694B14.5	cis	Whole Blood	GTEx
rs68165049	RP4-694B14.5	cis	Stomach	GTEx
rs68165049	ZNF337	cis	Whole Blood	GTEx
rs68165049	ZNF337	cis	Adipose Subcutaneous	GTEx
rs68165049	RP4-694B14.5	cis	Adipose Subcutaneous	GTEx
rs68165049	RP4-694B14.5	cis	Esophagus Muscularis	GTEx
rs68165049	NINL	cis	Nerve Tibial	GTEx
rs68165049	RP4-694B14.5	cis	Thyroid	GTEx
rs68165049	ZNF337	cis	Thyroid	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25493200-25512800	Weak transcription	Colon Smooth Muscle	Colon
2	chr20:25493600-25513000	Weak transcription	Left Ventricle	heart
3	chr20:25495800-25519400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr20:25496000-25512400	Weak transcription	Brain Angular Gyrus	brain
5	chr20:25496000-25513200	Weak transcription	HUVEC	blood vessel
6	chr20:25497400-25512400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr20:25497400-25512400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr20:25497400-25514800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr20:25497600-25512600	Weak transcription	Fetal Heart	heart
10	chr20:25497800-25512200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr20:25498200-25512200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr20:25498200-25512200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr20:25498200-25512600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr20:25498200-25512600	Weak transcription	Brain Anterior Caudate	brain
15	chr20:25498200-25512800	Weak transcription	Adipose Nuclei	Adipose
16	chr20:25498200-25513000	Weak transcription	Fetal Thymus	thymus
17	chr20:25498200-25514600	Weak transcription	Pancreas	Pancrea
18	chr20:25498200-25519000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr20:25498200-25519400	Weak transcription	Gastric	stomach
20	chr20:25498200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr20:25498400-25519200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr20:25498600-25512800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr20:25502600-25519800	Weak transcription	Stomach Mucosa	stomach
24	chr20:25502800-25513200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr20:25503400-25512400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr20:25504800-25512800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr20:25505000-25512800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr20:25505200-25512800	Weak transcription	Esophagus	oesophagus
29	chr20:25505200-25513800	Weak transcription	Fetal Kidney	kidney
30	chr20:25505400-25513000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr20:25505400-25514600	Weak transcription	Lung	lung
32	chr20:25505400-25521000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr20:25507000-25512800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr20:25507200-25512200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr20:25507200-25512400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr20:25507200-25512600	Weak transcription	Fetal Muscle Leg	muscle
37	chr20:25507200-25513400	Weak transcription	Fetal Lung	lung
38	chr20:25507400-25512200	Weak transcription	Thymus	Thymus
39	chr20:25507400-25512200	Weak transcription	Spleen	Spleen
40	chr20:25507400-25512400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr20:25507400-25512400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr20:25507400-25512600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr20:25507400-25512600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr20:25507400-25512800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr20:25507400-25518400	Weak transcription	A549	lung
46	chr20:25507600-25512200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr20:25507600-25512200	Weak transcription	Fetal Stomach	stomach
48	chr20:25507600-25512200	Weak transcription	Dnd41	blood
49	chr20:25507600-25512400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr20:25507600-25512400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links