Variant report

Variant	rs6540733
Chromosome Location	chr1:212392953-212392954
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212391958..212394846-chr1:212458658..212460726,2	K562	blood:
2	chr1:212374422..212376046-chr1:212392215..212393758,2	K562	blood:
3	chr1:212325848..212328405-chr1:212392780..212395278,2	K562	blood:

Variant related genes	Relation type
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1009622	0.83[CHB][hapmap]
rs10863953	0.87[EUR][1000 genomes]
rs10863954	0.88[EUR][1000 genomes]
rs11119879	0.88[EUR][1000 genomes]
rs11119880	0.83[EUR][1000 genomes]
rs11119883	0.90[EUR][1000 genomes]
rs11119884	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119887	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12028026	0.90[EUR][1000 genomes]
rs12038888	0.82[EUR][1000 genomes]
rs12073206	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12402397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12746096	0.81[EUR][1000 genomes]
rs1389369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1389370	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1389371	0.83[CHB][hapmap]
rs1472226	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1967114	0.88[EUR][1000 genomes]
rs1967116	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1967117	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2001234	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2087946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2307128	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2884512	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351386	0.83[CHB][hapmap]
rs351408	0.83[JPT][hapmap]
rs35209719	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816912	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4362041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4500383	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4558048	0.88[EUR][1000 genomes]
rs4951581	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951582	0.84[ASN][1000 genomes]
rs6540729	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6540731	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]
rs6540732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540734	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540735	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6657900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6668866	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6679064	0.80[EUR][1000 genomes]
rs6679796	0.83[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6695681	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7511781	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7515645	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7518329	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7519168	0.82[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530375	0.88[EUR][1000 genomes]
rs7537062	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7542973	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7544225	0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7552021	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs867584	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs903120	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs903121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs951623	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6540733	TMEM206	cis	Esophagus Mucosa	GTEx
rs6540733	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 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	chr1:212388600-212393000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:212388600-212393200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:212389000-212393000	Weak transcription	Fetal Intestine Large	intestine
6	chr1:212390800-212393800	Enhancers	Fetal Heart	heart
7	chr1:212391000-212393400	Enhancers	Stomach Mucosa	stomach
8	chr1:212391000-212393800	Enhancers	Fetal Thymus	thymus
9	chr1:212391000-212393800	Enhancers	Thymus	Thymus
10	chr1:212391000-212393800	Enhancers	NHDF-Ad	bronchial
11	chr1:212391200-212393000	Weak transcription	Placenta	Placenta
12	chr1:212391200-212393600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:212391200-212393800	Enhancers	HSMMtube	muscle
14	chr1:212391200-212394000	Enhancers	Fetal Kidney	kidney
15	chr1:212391200-212394000	Enhancers	Fetal Lung	lung
16	chr1:212391200-212399000	Weak transcription	Pancreas	Pancrea
17	chr1:212391600-212393400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:212391600-212393600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:212391600-212393800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:212391800-212393200	Enhancers	Primary T cells from cord blood	blood
21	chr1:212391800-212393400	Weak transcription	Lung	lung
22	chr1:212391800-212393800	Enhancers	HSMM	muscle
23	chr1:212392000-212393000	Weak transcription	Small Intestine	intestine
24	chr1:212392000-212393400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:212392000-212393600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:212392000-212393800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:212392000-212393800	Enhancers	NH-A	brain
28	chr1:212392000-212396000	Enhancers	K562	blood
29	chr1:212392000-212399400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:212392200-212393000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:212392200-212393200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:212392200-212393200	Weak transcription	Fetal Intestine Small	intestine
33	chr1:212392200-212393200	Enhancers	GM12878-XiMat	blood
34	chr1:212392200-212393600	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr1:212392200-212393800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:212392200-212395200	Weak transcription	Right Atrium	heart
37	chr1:212392200-212398600	Weak transcription	Right Ventricle	heart
38	chr1:212392200-212399000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:212392200-212399200	Weak transcription	Fetal Muscle Leg	muscle
40	chr1:212392400-212393400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:212392400-212393600	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr1:212392400-212394400	Weak transcription	Gastric	stomach
43	chr1:212392400-212397800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:212392400-212398600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:212392600-212393000	Weak transcription	Spleen	Spleen
46	chr1:212392600-212397400	Weak transcription	Adipose Nuclei	Adipose
47	chr1:212392600-212399000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:212392600-212399200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:212392600-212404800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr1:212392800-212393600	Enhancers	HUES48 Cell Line	embryonic stem cell

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