Variant report

Variant	rs1944937
Chromosome Location	chr11:74419357-74419358
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr11:74419301-74419358	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74108098..74110950-chr11:74416989..74419501,2	K562	blood:
2	chr11:74416357..74420489-chr11:74422265..74425552,4	K562	blood:

Variant related genes	Relation type
CHRDL2	TF binding region
ENSG00000165434	Chromatin interaction
ENSG00000264402	Chromatin interaction
ENSG00000254631	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10899039	0.86[ASN][1000 genomes]
rs10899040	0.91[CEU][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1433770	0.91[CEU][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs1893880	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1944936	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944945	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs7935154	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941425	0.87[EUR][1000 genomes]
rs948517	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[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	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats 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 miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv932190	chr11:74359867-74618935	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1944937	PAAF1	cis	cerebellum	SCAN
rs1944937	PLEKHB1	cis	cerebellum	SCAN
rs1944937	XRRA1	cis	cerebellum	SCAN
rs1944937	RAB6A	cis	parietal	SCAN
rs1944937	XRRA1	cis	lymphoblastoid	seeQTL
rs1944937	RNF169	cis	cerebellum	SCAN
rs1944937	XRRA1	cis	parietal	SCAN
rs1944937	P2RY2	cis	parietal	SCAN
rs1944937	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs1944937	FCHSD2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74407600-74421400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:74409000-74421400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr11:74409000-74421400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:74409000-74421400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:74409000-74421600	Weak transcription	Right Atrium	heart
6	chr11:74414000-74420800	Weak transcription	Colon Smooth Muscle	Colon
7	chr11:74414000-74421200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr11:74414600-74421600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:74417400-74422400	Enhancers	Placenta	Placenta
10	chr11:74418000-74420200	Enhancers	Fetal Intestine Large	intestine
11	chr11:74418200-74422600	Enhancers	Fetal Intestine Small	intestine
12	chr11:74418400-74419600	Enhancers	K562	blood
13	chr11:74418600-74419800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr11:74418800-74419400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:74418800-74419400	Enhancers	A549	lung
16	chr11:74418800-74419800	Enhancers	Ovary	ovary
17	chr11:74418800-74422600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr11:74419000-74422800	Enhancers	Fetal Stomach	stomach
19	chr11:74419200-74419400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:74419200-74419400	Enhancers	HSMMtube	muscle
21	chr11:74419200-74419600	Enhancers	Spleen	Spleen
22	chr11:74419200-74420000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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