Variant report

Variant	rs6540738
Chromosome Location	chr1:212557108-212557109
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212555152..212557714-chr1:212585836..212588272,2	MCF-7	breast:
2	chr1:212554525..212557472-chr1:212560250..212563380,3	K562	blood:

Variant related genes	Relation type
ENSG00000065600	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10863966	0.83[ASN][1000 genomes]
rs11119923	0.87[ASN][1000 genomes]
rs11811938	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12127560	0.85[ASN][1000 genomes]
rs1473321	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1539206	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28737261	0.84[ASN][1000 genomes]
rs3767866	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3767867	0.81[EUR][1000 genomes]
rs6540739	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6673357	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6678541	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6689309	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs765364	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6540738	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212502600-212563400	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr1:212502600-212564600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:212526800-212582800	Weak transcription	Fetal Brain Male	brain
4	chr1:212528400-212583000	Weak transcription	Fetal Kidney	kidney
5	chr1:212529400-212562400	Strong transcription	Dnd41	blood
6	chr1:212529800-212563200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:212532400-212560200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:212534000-212558200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:212534000-212570200	Weak transcription	HSMM	muscle
10	chr1:212534400-212570600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:212534600-212560000	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:212535000-212561400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:212535200-212560200	Weak transcription	Hela-S3	cervix
14	chr1:212536200-212561600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:212538000-212571000	Weak transcription	NH-A	brain
16	chr1:212538200-212559600	Weak transcription	Right Atrium	heart
17	chr1:212540400-212575400	Weak transcription	HUVEC	blood vessel
18	chr1:212540600-212562600	Weak transcription	Osteobl	bone
19	chr1:212540600-212564000	Weak transcription	Stomach Mucosa	stomach
20	chr1:212542800-212561600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:212543600-212565200	Weak transcription	Fetal Lung	lung
22	chr1:212545000-212561000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:212546800-212560200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:212546800-212560400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:212547000-212562600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:212547000-212563400	Strong transcription	Fetal Thymus	thymus
27	chr1:212547200-212561000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:212547400-212562400	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:212547400-212562400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:212548200-212560600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:212548600-212563800	Strong transcription	Primary T cells from cord blood	blood
32	chr1:212548800-212558800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:212549400-212560600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:212549400-212561000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr1:212549600-212560200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:212549800-212558600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:212550400-212561000	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:212550400-212562800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:212551000-212557800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:212551400-212561800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:212551600-212558000	Weak transcription	NHLF	lung
42	chr1:212551600-212560000	Weak transcription	Colonic Mucosa	Colon
43	chr1:212552000-212557600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr1:212552000-212559600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:212552000-212562000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:212552200-212557200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:212552400-212557600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr1:212553000-212562600	Strong transcription	GM12878-XiMat	blood
49	chr1:212553200-212557200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:212553200-212557200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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