Variant report

Variant	rs351393
Chromosome Location	chr1:212476519-212476520
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	chr1:212458179..212461162-chr1:212476171..212477846,2	K562	blood:

Variant related genes	Relation type
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11119904	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12023488	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12024665	0.88[ASN][1000 genomes]
rs12033246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12035647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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	0.96[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs1539206	0.81[YRI][hapmap]
rs17042034	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1774249	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1992643	0.96[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2252044	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2298114	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2516331	0.82[EUR][1000 genomes]
rs2589474	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3099112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[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]
rs351380	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs351386	1.00[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs351398	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs351401	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs351407	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs351408	1.00[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3767862	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3767863	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4951582	0.81[EUR][1000 genomes]
rs4951588	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4951589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs518793	1.00[YRI][hapmap]
rs6659594	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs701905	1.00[YRI][hapmap]
rs7415843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7519959	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7521853	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7544225	0.96[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs792445	0.86[EUR][1000 genomes]
rs792447	1.00[YRI][hapmap]
rs792448	0.89[ASW][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap]

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	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	esv1839887	chr1:212457414-212478047	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	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
9	nsv945282	chr1:212475737-212482732	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs351393	TMEM206	cis	lymphoblastoid	seeQTL
rs351393	TMEM206	cis	Esophagus Mucosa	GTEx
rs351393	TMEM206	cis	cerebellum	SCAN
rs351393	LGTN	cis	cerebellum	SCAN
rs351393	SLC30A1	cis	cerebellum	SCAN
rs351393	TMEM206	cis	parietal	SCAN
rs351393	NENF	cis	Esophagus Mucosa	GTEx
rs351393	CD34	cis	cerebellum	SCAN

Chromatin state (count:69 , 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	chr1:212464800-212480200	Weak transcription	Lung	lung
4	chr1:212464800-212483800	Weak transcription	Pancreas	Pancrea
5	chr1:212464800-212506400	Weak transcription	Esophagus	oesophagus
6	chr1:212465000-212480200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:212465400-212482800	Weak transcription	Fetal Lung	lung
8	chr1:212465800-212483200	Weak transcription	Dnd41	blood
9	chr1:212466200-212506400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:212466600-212479400	Weak transcription	NHEK	skin
11	chr1:212466600-212482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:212466600-212503000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:212467000-212480800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:212467200-212481800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr1:212467400-212480200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr1:212467400-212482800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:212467400-212526000	Weak transcription	A549	lung
18	chr1:212467600-212482800	Weak transcription	HepG2	liver
19	chr1:212468800-212478200	Weak transcription	Fetal Intestine Small	intestine
20	chr1:212469000-212480200	Weak transcription	Fetal Intestine Large	intestine
21	chr1:212469000-212483200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:212469000-212483400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:212470000-212481800	Weak transcription	Thymus	Thymus
24	chr1:212470400-212481200	Weak transcription	Primary T cells from cord blood	blood
25	chr1:212470800-212482600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:212472600-212478200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr1:212473400-212477000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:212473400-212477800	Weak transcription	Psoas Muscle	Psoas
29	chr1:212473400-212483800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:212473600-212478800	Weak transcription	Small Intestine	intestine
31	chr1:212474000-212477600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr1:212474200-212476600	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr1:212474200-212484000	Weak transcription	Primary B cells from cord blood	blood
34	chr1:212474200-212502800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:212474400-212477200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr1:212474600-212477800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr1:212474600-212477800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:212474600-212482400	Weak transcription	Left Ventricle	heart
39	chr1:212474600-212482600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:212474600-212489200	Weak transcription	Gastric	stomach
41	chr1:212474800-212477400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:212474800-212482400	Weak transcription	Right Atrium	heart
43	chr1:212474800-212483400	Weak transcription	Right Ventricle	heart
44	chr1:212475200-212476600	Weak transcription	Osteobl	bone
45	chr1:212475200-212480600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:212475200-212482400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:212475200-212483000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:212475200-212483200	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:212475200-212483800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:212475200-212487000	Weak transcription	HSMMtube	muscle

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