Variant report

Variant	rs884786
Chromosome Location	chr12:122473182-122473183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122472899..122475039-chr12:122517716..122519220,2	MCF-7	breast:
2	chr12:122472104..122474450-chr12:122476458..122479458,3	K562	blood:
3	chr12:122450006..122452585-chr12:122472596..122474160,2	K562	blood:
4	chr12:122471389..122473549-chr12:122630126..122632348,2	K562	blood:
5	chr12:122471870..122474325-chr12:122611041..122613335,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175727	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1824949	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1851597	0.90[EUR][1000 genomes]
rs2076860	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2272132	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741581	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4522209	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs55778445	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57298119	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58025403	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58026220	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58158474	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58516770	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59116149	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59178789	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60620185	0.84[EUR][1000 genomes]
rs6486792	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6486793	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7138299	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7294535	0.84[EUR][1000 genomes]
rs7294829	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7314352	0.84[EUR][1000 genomes]
rs7964151	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs830125	0.84[EUR][1000 genomes]
rs872781	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs884785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription 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	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs884786	RBM46	trans	lymphoblastoid	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122461600-122492400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:122461800-122473200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:122461800-122476600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:122462000-122473200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:122462000-122473400	Weak transcription	Primary T cells from cord blood	blood
6	chr12:122462000-122492400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr12:122462200-122473200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:122462200-122473400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:122462200-122474200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr12:122462200-122489000	Weak transcription	HUVEC	blood vessel
11	chr12:122462400-122473200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:122462400-122473200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:122462400-122473200	Weak transcription	Aorta	Aorta
14	chr12:122462400-122473200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr12:122462400-122477800	Weak transcription	Fetal Kidney	kidney
16	chr12:122462400-122481800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:122462400-122489000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:122462400-122490400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr12:122462400-122492200	Weak transcription	Stomach Mucosa	stomach
20	chr12:122462400-122500000	Weak transcription	Hela-S3	cervix
21	chr12:122462600-122478000	Weak transcription	Colon Smooth Muscle	Colon
22	chr12:122465200-122473200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:122466200-122500800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr12:122466400-122473600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:122466400-122489000	Weak transcription	NHLF	lung
26	chr12:122466800-122490200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:122467000-122480600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr12:122467400-122473200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr12:122467800-122473200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr12:122467800-122478000	Strong transcription	Fetal Intestine Small	intestine
31	chr12:122467800-122488800	Weak transcription	Right Atrium	heart
32	chr12:122467800-122500000	Strong transcription	Thymus	Thymus
33	chr12:122467800-122500200	Strong transcription	Dnd41	blood
34	chr12:122468000-122473200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:122468000-122473200	Weak transcription	Liver	Liver
36	chr12:122468000-122473800	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:122468000-122489200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:122468200-122473400	Weak transcription	Brain Substantia Nigra	brain
39	chr12:122468200-122492800	Weak transcription	NHDF-Ad	bronchial
40	chr12:122468400-122473400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:122468400-122474000	Weak transcription	Ovary	ovary
42	chr12:122468400-122486000	Weak transcription	NH-A	brain
43	chr12:122468400-122489000	Strong transcription	Fetal Stomach	stomach
44	chr12:122468400-122489000	Weak transcription	Psoas Muscle	Psoas
45	chr12:122468600-122473200	Weak transcription	HSMMtube	muscle
46	chr12:122468600-122478000	Weak transcription	HepG2	liver
47	chr12:122468800-122474000	Weak transcription	HSMM	muscle
48	chr12:122468800-122474800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr12:122469800-122473800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr12:122469800-122481800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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