Variant report

Variant	rs6540731
Chromosome Location	chr1:212392163-212392164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212391958..212394846-chr1:212458658..212460726,2	K562	blood:

Variant related genes	Relation type
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1009622	0.91[CHB][hapmap];0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs10436962	0.80[EUR][1000 genomes]
rs10436976	0.80[EUR][1000 genomes]
rs10863953	0.88[EUR][1000 genomes]
rs10863954	0.88[EUR][1000 genomes]
rs11119879	0.88[EUR][1000 genomes]
rs11119880	0.83[EUR][1000 genomes]
rs11119883	0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs11119884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119885	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119887	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12028026	0.91[EUR][1000 genomes]
rs12038888	0.83[EUR][1000 genomes]
rs12073206	0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs12402397	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12746096	0.81[EUR][1000 genomes]
rs1389369	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1389370	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1389371	0.82[CHD][hapmap]
rs1472226	0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1967114	0.89[EUR][1000 genomes]
rs1967116	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1967117	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2001234	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2012917	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2087946	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2307128	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2884512	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs351386	0.91[CHB][hapmap];0.85[CHD][hapmap]
rs351408	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs35209719	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3816912	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4362041	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4500383	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4558048	0.88[EUR][1000 genomes]
rs4951581	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4951582	0.85[ASN][1000 genomes]
rs6540729	0.89[EUR][1000 genomes]
rs6540732	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540733	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540734	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540735	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6657900	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6668866	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]
rs6679796	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6695681	0.90[EUR][1000 genomes]
rs7511781	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515645	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518329	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7519168	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7530375	0.88[EUR][1000 genomes]
rs7537062	0.90[EUR][1000 genomes]
rs7542973	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7544225	0.91[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs7552021	0.89[EUR][1000 genomes]
rs867584	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs903120	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs903121	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs951623	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

Variant related diseases (count:1)

Disease	PMID	Source
Intelligence (childhood)	23358156	GWAS catalog

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6540731	C1orf74	cis	cerebellum	SCAN
rs6540731	LGTN	cis	cerebellum	SCAN
rs6540731	TMEM206	cis	Esophagus Mucosa	GTEx
rs6540731	FCAMR	cis	parietal	SCAN
rs6540731	TMEM206	cis	cerebellum	SCAN
rs6540731	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs6540731	NSL1	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212383000-212393000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:212383400-212394600	Weak transcription	Left Ventricle	heart
3	chr1:212388600-212392400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr1:212388600-212393000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:212388600-212393200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:212389000-212393000	Weak transcription	Fetal Intestine Large	intestine
7	chr1:212390800-212392600	Enhancers	Adipose Nuclei	Adipose
8	chr1:212390800-212393800	Enhancers	Fetal Heart	heart
9	chr1:212391000-212392200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:212391000-212392200	Enhancers	Fetal Intestine Small	intestine
11	chr1:212391000-212392200	Enhancers	Fetal Muscle Leg	muscle
12	chr1:212391000-212392200	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr1:212391000-212392400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:212391000-212392600	Enhancers	HUVEC	blood vessel
15	chr1:212391000-212393400	Enhancers	Stomach Mucosa	stomach
16	chr1:212391000-212393800	Enhancers	Fetal Thymus	thymus
17	chr1:212391000-212393800	Enhancers	Thymus	Thymus
18	chr1:212391000-212393800	Enhancers	NHDF-Ad	bronchial
19	chr1:212391200-212392200	Enhancers	Right Atrium	heart
20	chr1:212391200-212392200	Bivalent Enhancer	HepG2	liver
21	chr1:212391200-212392400	Enhancers	Gastric	stomach
22	chr1:212391200-212392600	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr1:212391200-212392600	Enhancers	Spleen	Spleen
24	chr1:212391200-212392800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:212391200-212393000	Weak transcription	Placenta	Placenta
26	chr1:212391200-212393600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:212391200-212393800	Enhancers	HSMMtube	muscle
28	chr1:212391200-212394000	Enhancers	Fetal Kidney	kidney
29	chr1:212391200-212394000	Enhancers	Fetal Lung	lung
30	chr1:212391200-212399000	Weak transcription	Pancreas	Pancrea
31	chr1:212391400-212392400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:212391400-212392600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:212391600-212392200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:212391600-212392800	Enhancers	Osteobl	bone
35	chr1:212391600-212393400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:212391600-212393600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:212391600-212393800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:212391800-212392200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:212391800-212392200	Flanking Active TSS	GM12878-XiMat	blood
40	chr1:212391800-212392400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:212391800-212392600	Enhancers	Primary B cells from peripheral blood	blood
42	chr1:212391800-212392600	Enhancers	Dnd41	blood
43	chr1:212391800-212393200	Enhancers	Primary T cells from cord blood	blood
44	chr1:212391800-212393400	Weak transcription	Lung	lung
45	chr1:212391800-212393800	Enhancers	HSMM	muscle
46	chr1:212392000-212392200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:212392000-212392200	Enhancers	Right Ventricle	heart
48	chr1:212392000-212392400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:212392000-212392600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
50	chr1:212392000-212393000	Weak transcription	Small Intestine	intestine

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