Variant report

Variant	rs12363645
Chromosome Location	chr11:9340899-9340900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr11:9340789-9341094	K562	blood:	n/a	n/a
2	SP1	chr11:9340739-9341297	A549	lung:	n/a	n/a
3	CBX3	chr11:9340528-9341156	K562	blood:	n/a	n/a
4	SPI1	chr11:9340627-9340926	K562	blood:	n/a	n/a
5	HEY1	chr11:9340530-9341034	K562	blood:	n/a	n/a
6	SPI1	chr11:9340621-9340935	K562	blood:	n/a	n/a
7	NR3C1	chr11:9340832-9341317	A549	lung:	n/a	n/a
8	CEBPD	chr11:9340574-9341088	K562	blood:	n/a	n/a
9	FOXA2	chr11:9340789-9341361	A549	lung:	n/a	n/a
10	POLR2A	chr11:9340333-9341110	H1-hESC	embryonic stem cell:	n/a	n/a
11	NR2F2	chr11:9340652-9341396	K562	blood:	n/a	n/a
12	FOXA2	chr11:9340763-9341314	A549	lung:	n/a	n/a
13	NR3C1	chr11:9340850-9341295	A549	lung:	n/a	n/a
14	MYC	chr11:9340572-9341252	K562	blood:	n/a	chr11:9341092-9341102
15	MAX	chr11:9340895-9341129	K562	blood:	n/a	chr11:9341092-9341102
16	GATA2	chr11:9340416-9341089	K562	blood:	n/a	n/a
17	TEAD4	chr11:9340552-9341097	K562	blood:	n/a	n/a
18	MAX	chr11:9340818-9341435	K562	blood:	n/a	chr11:9341092-9341102
19	TAL1	chr11:9340784-9341092	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:9335954..9337898-chr11:9338868..9341864,2	MCF-7	breast:
2	chr11:9340099..9341821-chr11:9406076..9407698,2	K562	blood:
3	chr11:9339910..9342250-chr11:9383907..9387311,3	K562	blood:
4	chr11:9340099..9343454-chr11:9406076..9407743,3	K562	blood:

No data

Variant related genes	Relation type
TMEM41B	TF binding region
ENSG00000166471	Chromatin interaction
ENSG00000205339	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10454487	0.84[EUR][1000 genomes]
rs11042240	0.80[EUR][1000 genomes]
rs11042241	0.81[EUR][1000 genomes]
rs11042246	0.81[EUR][1000 genomes]
rs11042253	0.83[EUR][1000 genomes]
rs11042257	0.84[EUR][1000 genomes]
rs11042259	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042268	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042272	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12362997	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12807631	1.00[ASN][1000 genomes]
rs17257379	0.83[EUR][1000 genomes]
rs4627079	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910446	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910447	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55962227	0.81[EUR][1000 genomes]
rs7103472	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7115283	0.81[EUR][1000 genomes]
rs7115373	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72850512	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72850528	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72850531	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72850544	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72850552	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72861335	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72861360	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7936622	0.83[EUR][1000 genomes]
rs7938562	0.81[EUR][1000 genomes]
rs7939704	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940872	0.83[EUR][1000 genomes]
rs7945570	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9645644	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040049	chr11:9152536-9363488	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1053045	chr11:9208881-9363488	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv540947	chr11:9208881-9363488	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1055078	chr11:9252857-9538877	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
6	nsv508617	chr11:9314027-9408562	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
7	nsv521969	chr11:9334961-9379005	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12363645	TMEM41B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9337000-9341200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr11:9337000-9341400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:9337000-9350600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr11:9337200-9341200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:9337200-9341200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:9337200-9341200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:9337200-9341200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:9337200-9341400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr11:9337200-9350400	Weak transcription	HSMMtube	muscle
10	chr11:9337400-9342800	Enhancers	K562	blood
11	chr11:9339000-9341000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr11:9339400-9341800	Enhancers	Stomach Mucosa	stomach
13	chr11:9339800-9341400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr11:9339800-9341600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr11:9339800-9341800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr11:9339800-9341800	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr11:9339800-9342000	Enhancers	HepG2	liver
18	chr11:9340000-9342000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:9340000-9342000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr11:9340200-9341800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr11:9340400-9341000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr11:9340400-9341000	Enhancers	Duodenum Mucosa	Duodenum
23	chr11:9340400-9341200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:9340400-9341200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr11:9340400-9341400	Weak transcription	Lung	lung
26	chr11:9340600-9341000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr11:9340600-9341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr11:9340600-9341000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr11:9340600-9341000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr11:9340600-9341000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr11:9340600-9341000	Weak transcription	Fetal Intestine Large	intestine
32	chr11:9340600-9341000	Weak transcription	Fetal Intestine Small	intestine
33	chr11:9340600-9341200	Enhancers	A549	lung
34	chr11:9340600-9341600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:9340800-9341800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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