Variant report

Variant	rs351380
Chromosome Location	chr1:212482852-212482853
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	chr1:212457668..212459740-chr1:212480446..212483252,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10019	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11119904	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12023488	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12024665	0.89[ASN][1000 genomes]
rs12033246	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12035647	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036130	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12410664	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1389371	0.82[EUR][1000 genomes]
rs17042034	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1774249	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1992643	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2252044	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2298114	0.96[ASN][1000 genomes]
rs2516331	0.82[EUR][1000 genomes]
rs2589474	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3099112	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs351373	0.82[EUR][1000 genomes]
rs351377	0.82[EUR][1000 genomes]
rs351378	0.82[EUR][1000 genomes]
rs351379	0.82[EUR][1000 genomes]
rs351386	0.82[EUR][1000 genomes]
rs351393	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs351398	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs351401	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs351407	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs351408	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs351417	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs351419	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3767861	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3767862	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3767863	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4951582	0.81[EUR][1000 genomes]
rs4951588	0.89[ASN][1000 genomes]
rs4951589	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6659594	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7415843	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7519959	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7521853	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7544225	0.82[EUR][1000 genomes]
rs792445	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers 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	45 gene(s)	inside rSNPs	diseases
6	nsv873155	chr1:212449195-212502157	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1806604	chr1:212468974-212505860	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs351380	TMEM206	cis	Esophagus Mucosa	GTEx
rs351380	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs351380	NENF	cis	Esophagus Mucosa	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212460200-212489200	Weak transcription	Spleen	Spleen
2	chr1:212464200-212483000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:212464800-212483800	Weak transcription	Pancreas	Pancrea
4	chr1:212464800-212506400	Weak transcription	Esophagus	oesophagus
5	chr1:212465800-212483200	Weak transcription	Dnd41	blood
6	chr1:212466200-212506400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:212466600-212503000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:212467400-212526000	Weak transcription	A549	lung
9	chr1:212469000-212483200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:212469000-212483400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:212473400-212483800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:212474200-212484000	Weak transcription	Primary B cells from cord blood	blood
13	chr1:212474200-212502800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:212474600-212489200	Weak transcription	Gastric	stomach
15	chr1:212474800-212483400	Weak transcription	Right Ventricle	heart
16	chr1:212475200-212483000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:212475200-212483200	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:212475200-212483800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:212475200-212487000	Weak transcription	HSMMtube	muscle
20	chr1:212475400-212483600	Weak transcription	Brain Angular Gyrus	brain
21	chr1:212475400-212487000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:212475600-212483400	Weak transcription	Adipose Nuclei	Adipose
23	chr1:212475600-212483400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:212475600-212488600	Weak transcription	Fetal Heart	heart
25	chr1:212476000-212483000	Weak transcription	Brain Substantia Nigra	brain
26	chr1:212476800-212483200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:212477000-212483800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:212477000-212484000	Weak transcription	Osteobl	bone
29	chr1:212477200-212483200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:212478200-212495800	Weak transcription	Fetal Thymus	thymus
31	chr1:212478400-212483200	Weak transcription	Psoas Muscle	Psoas
32	chr1:212479200-212525400	Weak transcription	Aorta	Aorta
33	chr1:212479600-212489000	Weak transcription	Small Intestine	intestine
34	chr1:212479600-212489200	Weak transcription	Stomach Mucosa	stomach
35	chr1:212479800-212483400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:212479800-212484600	Weak transcription	NHEK	skin
37	chr1:212480200-212484400	Strong transcription	Fetal Intestine Large	intestine
38	chr1:212480400-212483400	Weak transcription	Lung	lung
39	chr1:212480400-212484000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr1:212480400-212484800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:212480400-212485400	Weak transcription	HMEC	breast
42	chr1:212480600-212484200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:212480600-212489400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr1:212480800-212488400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:212481200-212483000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:212481200-212484000	Strong transcription	Fetal Stomach	stomach
47	chr1:212481200-212484200	Weak transcription	Placenta	Placenta
48	chr1:212481200-212484600	Strong transcription	Primary T cells from cord blood	blood
49	chr1:212481400-212483200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:212481400-212484800	Strong transcription	Fetal Intestine Small	intestine

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