Variant report

Variant	rs6540729
Chromosome Location	chr1:212387908-212387909
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212386318..212388694-chr1:212411240..212413390,2	K562	blood:

Variant related genes	Relation type
ENSG00000226251	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10779575	0.95[ASN][1000 genomes]
rs10863953	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10863954	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11119879	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11119883	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119884	0.87[EUR][1000 genomes]
rs11119885	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12028026	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12073206	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12402397	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1389369	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1389370	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1472226	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1967114	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1967116	0.80[EUR][1000 genomes]
rs2001234	0.81[EUR][1000 genomes]
rs2012917	0.86[EUR][1000 genomes]
rs2087946	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2884512	0.83[EUR][1000 genomes]
rs35209719	0.88[EUR][1000 genomes]
rs3816912	0.88[EUR][1000 genomes]
rs4362041	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4500383	0.89[EUR][1000 genomes]
rs4558048	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4951581	0.87[EUR][1000 genomes]
rs6540731	0.89[EUR][1000 genomes]
rs6540732	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6540733	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6540734	0.87[EUR][1000 genomes]
rs6540735	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6657900	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6695681	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511781	0.86[EUR][1000 genomes]
rs7515645	0.88[EUR][1000 genomes]
rs7518329	0.86[EUR][1000 genomes]
rs7530375	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7537062	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552021	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867584	0.82[EUR][1000 genomes]
rs903120	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs903121	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs951623	0.88[EUR][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
rs6540729	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs6540729	TMEM206	cis	Esophagus Mucosa	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212368800-212391000	Weak transcription	Thymus	Thymus
2	chr1:212379600-212391600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:212381800-212391200	Weak transcription	Right Atrium	heart
4	chr1:212382800-212388800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:212382800-212391000	Weak transcription	Stomach Mucosa	stomach
6	chr1:212383000-212393000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:212383400-212394600	Weak transcription	Left Ventricle	heart
8	chr1:212386200-212388800	Enhancers	Fetal Intestine Small	intestine
9	chr1:212386400-212391200	Weak transcription	Fetal Kidney	kidney
10	chr1:212387200-212388600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr1:212387200-212388600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:212387200-212389000	Enhancers	Fetal Intestine Large	intestine
13	chr1:212387200-212389000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr1:212387200-212389000	Enhancers	K562	blood
15	chr1:212387400-212388000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:212387400-212388000	Enhancers	Duodenum Mucosa	Duodenum
17	chr1:212387600-212388200	Weak transcription	Colonic Mucosa	Colon
18	chr1:212387600-212388600	Enhancers	Fetal Thymus	thymus
19	chr1:212387600-212389000	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr1:212387600-212391200	Weak transcription	Spleen	Spleen
21	chr1:212387800-212388600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr1:212387800-212390800	Weak transcription	Adipose Nuclei	Adipose

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