Variant report

Variant	rs6668866
Chromosome Location	chr1:212404947-212404948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212404572..212406195-chr1:212406455..212408125,2	K562	blood:
2	chr1:212404478..212406479-chr1:212423764..212425331,2	K562	blood:
3	chr1:212404851..212407731-chr1:212434475..212437929,3	K562	blood:

Variant related genes	Relation type
ENSG00000226251	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1009622	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs10436962	0.90[EUR][1000 genomes]
rs10436976	0.90[EUR][1000 genomes]
rs11119880	0.95[EUR][1000 genomes]
rs11119884	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119885	0.92[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11119887	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12038888	0.93[EUR][1000 genomes]
rs12041554	0.87[EUR][1000 genomes]
rs12402397	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12746096	0.91[EUR][1000 genomes]
rs1389369	0.92[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1389370	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1389371	0.86[CHD][hapmap];0.89[JPT][hapmap]
rs1472226	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1967116	0.96[ASN][1000 genomes]
rs1967117	0.96[ASN][1000 genomes]
rs2001234	0.96[ASN][1000 genomes]
rs2012917	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2087946	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2307128	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2358452	0.89[EUR][1000 genomes]
rs2884512	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351373	0.81[ASN][1000 genomes]
rs351377	0.82[ASN][1000 genomes]
rs351378	0.82[ASN][1000 genomes]
rs351379	0.82[ASN][1000 genomes]
rs351386	0.91[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs351408	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs35209719	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3816912	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4362041	0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4500383	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4951581	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951582	0.88[ASN][1000 genomes]
rs6540731	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540732	0.92[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6540733	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6540734	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540735	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6657900	0.92[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6679064	0.90[EUR][1000 genomes]
rs6679796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511781	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7515645	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7518329	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7519168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7542973	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7544225	0.91[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs867584	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs903120	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs903121	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs951623	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6668866	LGTN	cis	cerebellum	SCAN
rs6668866	TMEM206	cis	Esophagus Mucosa	GTEx
rs6668866	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs6668866	CD34	cis	cerebellum	SCAN
rs6668866	TMEM206	cis	cerebellum	SCAN
rs6668866	SYT14	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212399400-212405200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr1:212399800-212405200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr1:212399800-212406600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:212399800-212407800	Weak transcription	Brain Anterior Caudate	brain
5	chr1:212400000-212405000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:212400000-212405200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:212400000-212405200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:212400000-212405200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:212400000-212405200	Weak transcription	Fetal Thymus	thymus
10	chr1:212400000-212407600	Weak transcription	Spleen	Spleen
11	chr1:212400000-212407800	Weak transcription	Right Atrium	heart
12	chr1:212400000-212407800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:212400200-212405400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:212400200-212406800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:212401400-212408400	Weak transcription	Lung	lung
16	chr1:212401600-212405000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:212401800-212409000	Weak transcription	Gastric	stomach
18	chr1:212402400-212407800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:212402800-212405800	Enhancers	Stomach Mucosa	stomach
20	chr1:212403400-212405600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:212403400-212409000	Weak transcription	Fetal Intestine Large	intestine
22	chr1:212403600-212407000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:212403600-212407600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:212403600-212408200	Weak transcription	Small Intestine	intestine
25	chr1:212403600-212409600	Weak transcription	Liver	Liver
26	chr1:212403800-212407600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:212403800-212407600	Weak transcription	NHDF-Ad	bronchial
28	chr1:212403800-212407600	Weak transcription	Osteobl	bone
29	chr1:212404000-212407200	Weak transcription	Right Ventricle	heart
30	chr1:212404400-212405200	Enhancers	HepG2	liver
31	chr1:212404400-212405800	Enhancers	K562	blood
32	chr1:212404600-212405600	Enhancers	Esophagus	oesophagus
33	chr1:212404600-212405600	Enhancers	Pancreas	Pancrea
34	chr1:212404600-212405800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:212404600-212407800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:212404800-212405000	Enhancers	Fetal Muscle Leg	muscle
37	chr1:212404800-212405200	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr1:212404800-212405400	Enhancers	Fetal Heart	heart
39	chr1:212404800-212405600	Enhancers	Left Ventricle	heart
40	chr1:212404800-212405800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr1:212404800-212410800	Enhancers	Skeletal Muscle Male	skeletal muscle

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