Variant report

Variant	rs3889743
Chromosome Location	chr11:85863683-85863684
allele	C/G
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	TEAD4	chr11:85862525-85863816	SK-N-SH	brain:	n/a	n/a
2	ZNF143	chr11:85863481-85863833	K562	blood:	n/a	n/a
3	TEAD4	chr11:85862499-85863857	SK-N-SH	brain:	n/a	n/a
4	PBX3	chr11:85862475-85863770	SK-N-SH	brain:	n/a	chr11:85863700-85863709
5	FOSL2	chr11:85863194-85863723	SK-N-SH	brain:	n/a	chr11:85863427-85863434
6	RXRA	chr11:85862415-85863708	SK-N-SH	brain:	n/a	chr11:85862857-85862870 chr11:85862858-85862869 chr11:85862857-85862870
7	EP300	chr11:85861922-85863871	SK-N-SH	brain:	n/a	chr11:85862141-85862150
8	PBX3	chr11:85862468-85863860	SK-N-SH	brain:	n/a	chr11:85863700-85863709
9	TCF12	chr11:85861737-85863866	SK-N-SH	brain:	n/a	n/a
10	RCOR1	chr11:85863454-85863918	K562	blood:	n/a	n/a
11	GATA3	chr11:85861779-85863825	SK-N-SH	brain:	n/a	chr11:85862582-85862591 chr11:85862579-85862595 chr11:85863030-85863040 chr11:85862579-85862595
12	TEAD4	chr11:85863204-85863721	ECC-1	luminal epithelium:	n/a	n/a
13	TEAD4	chr11:85862924-85863769	ECC-1	luminal epithelium:	n/a	n/a
14	EP300	chr11:85863605-85863802	K562	blood:	n/a	n/a
15	NFIC	chr11:85861769-85863775	SK-N-SH	brain:	n/a	chr11:85862353-85862370
16	NFIC	chr11:85862017-85863706	ECC-1	luminal epithelium:	n/a	chr11:85862353-85862370
17	NFIC	chr11:85861994-85863791	ECC-1	luminal epithelium:	n/a	chr11:85862353-85862370
18	EP300	chr11:85861991-85863778	ECC-1	luminal epithelium:	n/a	chr11:85862141-85862150
19	ZNF143	chr11:85863467-85863711	GM12878	blood:	n/a	n/a
20	GATA3	chr11:85862375-85863856	SK-N-SH	brain:	n/a	chr11:85862582-85862591 chr11:85862579-85862595 chr11:85863030-85863040 chr11:85862579-85862595
21	TCF12	chr11:85861702-85863757	SK-N-SH	brain:	n/a	n/a
22	RCOR1	chr11:85863378-85863687	Hela-S3	cervix:	n/a	n/a
23	RXRA	chr11:85862553-85863733	SK-N-SH	brain:	n/a	chr11:85862857-85862870 chr11:85862858-85862869 chr11:85862857-85862870
24	JUND	chr11:85862495-85863740	SK-N-SH	brain:	n/a	chr11:85863427-85863434

No.	Distal block	Cell Line	Cell type
1	chr11:85859696..85863993-chr11:85872249..85875647,5	K562	blood:
2	chr11:85773252..85777138-chr11:85860597..85863727,3	K562	blood:
3	chr11:85779872..85782905-chr11:85861004..85863950,3	K562	blood:
4	chr11:85779554..85782905-chr11:85860304..85865248,6	K562	blood:

Variant related genes	Relation type
RNU6-560P	TF binding region
ENSG00000073921	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10160337	0.95[MKK][hapmap];0.88[YRI][hapmap]
rs10160830	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10501611	1.00[CEU][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17745564	1.00[EUR][1000 genomes]
rs56084917	1.00[EUR][1000 genomes]
rs56371467	1.00[EUR][1000 genomes]
rs56411296	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[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	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv832223	chr11:85845315-86015957	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3889743	GSTM3	trans	lymphoblastoid	seeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85861000-85863800	Enhancers	Ovary	ovary
2	chr11:85861000-85864600	Enhancers	Fetal Lung	lung
3	chr11:85861200-85863800	Enhancers	Aorta	Aorta
4	chr11:85861200-85864000	Enhancers	Colon Smooth Muscle	Colon
5	chr11:85861200-85864200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:85861200-85864200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:85861200-85864200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr11:85861200-85864200	Enhancers	Fetal Stomach	stomach
9	chr11:85861200-85864400	Enhancers	Fetal Intestine Large	intestine
10	chr11:85861400-85863800	Enhancers	Fetal Muscle Leg	muscle
11	chr11:85861400-85863800	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr11:85861400-85865200	Enhancers	Liver	Liver
13	chr11:85861600-85864200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:85861600-85864200	Enhancers	Rectal Smooth Muscle	rectum
15	chr11:85861600-85864400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:85861800-85863800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:85861800-85863800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:85861800-85863800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:85861800-85863800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr11:85861800-85864000	Enhancers	Adipose Nuclei	Adipose
21	chr11:85861800-85864800	Enhancers	Duodenum Mucosa	Duodenum
22	chr11:85861800-85865200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:85862000-85863800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:85862000-85863800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:85862000-85863800	Enhancers	Primary T cells fromperipheralblood	blood
26	chr11:85862000-85863800	Enhancers	Placenta	Placenta
27	chr11:85862000-85864200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr11:85862000-85864800	Enhancers	Fetal Kidney	kidney
29	chr11:85862000-85865200	Enhancers	Fetal Intestine Small	intestine
30	chr11:85862200-85863800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr11:85862200-85863800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr11:85862200-85863800	Enhancers	Psoas Muscle	Psoas
33	chr11:85862200-85863800	Flanking Active TSS	HSMM	muscle
34	chr11:85862200-85864000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr11:85862200-85864400	Enhancers	Primary hematopoietic stem cells	blood
36	chr11:85862200-85864800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr11:85862400-85863800	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr11:85862400-85865200	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr11:85862600-85863800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:85862600-85864000	Enhancers	HSMMtube	muscle
41	chr11:85862600-85864400	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr11:85862600-85867400	Weak transcription	Pancreas	Pancrea
43	chr11:85862800-85863800	Bivalent Enhancer	Dnd41	blood
44	chr11:85862800-85864400	Enhancers	HMEC	breast
45	chr11:85863000-85864200	Enhancers	HUVEC	blood vessel
46	chr11:85863000-85867600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr11:85863200-85864000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr11:85863200-85864000	Weak transcription	Small Intestine	intestine
49	chr11:85863200-85864200	Enhancers	Brain Cingulate Gyrus	brain
50	chr11:85863200-85864200	Enhancers	NHEK	skin

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