Variant report

Variant	rs7233980
Chromosome Location	chr18:9596424-9596425
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr18:9596084-9596758	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr18:9596224-9596738	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr18:9596062-9596805	SK-N-SH	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:9594858..9597558-chr18:9614248..9616397,2	MCF-7	breast:
2	chr18:9581775..9584005-chr18:9596096..9598190,2	K562	blood:
3	chr18:9595087..9597869-chr18:9607007..9610720,3	MCF-7	breast:
4	chr18:9596087..9600746-chr18:9613522..9617540,6	MCF-7	breast:
5	chr18:9593612..9595267-chr18:9595493..9597647,2	K562	blood:

No data

Variant related genes	Relation type
PPP4R1	TF binding region
ENSG00000263627	Chromatin interaction
ENSG00000154845	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11081483	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12962253	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12970116	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12970514	1.00[JPT][hapmap]
rs1596381	0.95[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867167	0.95[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs4438368	0.87[EUR][1000 genomes]
rs6506676	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8087795	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8093596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv543644	chr18:9576145-9612516	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7233980	APCDD1	cis	cerebellum	SCAN
rs7233980	SEH1L	cis	cerebellum	SCAN
rs7233980	AFG3L2	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9551000-9612200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr18:9553800-9613600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:9576200-9597800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr18:9581400-9609200	Weak transcription	Pancreas	Pancrea
5	chr18:9582000-9597000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr18:9582800-9597600	Weak transcription	Fetal Brain Male	brain
7	chr18:9584800-9596600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr18:9585000-9597200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr18:9588600-9612400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr18:9589000-9596800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr18:9589000-9597200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr18:9589000-9597200	Weak transcription	Ovary	ovary
13	chr18:9589000-9608800	Weak transcription	Thymus	Thymus
14	chr18:9589000-9609200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr18:9589000-9611000	Weak transcription	Lung	lung
16	chr18:9589200-9598200	Weak transcription	Primary B cells from cord blood	blood
17	chr18:9589200-9599200	Weak transcription	Fetal Kidney	kidney
18	chr18:9590800-9597600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr18:9591600-9597000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr18:9592000-9597400	Weak transcription	Fetal Brain Female	brain
21	chr18:9592400-9597000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr18:9592400-9599400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr18:9592600-9597000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr18:9592600-9599800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr18:9593000-9598800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr18:9594000-9596600	Weak transcription	Primary T cells from cord blood	blood
27	chr18:9594000-9597200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr18:9594000-9597600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr18:9594000-9599400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr18:9594200-9596600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr18:9594200-9597000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr18:9594200-9597400	Weak transcription	Brain Germinal Matrix	brain
33	chr18:9594200-9600400	Weak transcription	Placenta	Placenta
34	chr18:9594200-9600400	Weak transcription	Fetal Stomach	stomach
35	chr18:9594200-9600600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr18:9594200-9609200	Weak transcription	Aorta	Aorta
37	chr18:9594200-9613600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr18:9594400-9596600	Enhancers	Rectal Smooth Muscle	rectum
39	chr18:9594400-9596800	Enhancers	Colon Smooth Muscle	Colon
40	chr18:9594400-9597000	Weak transcription	Fetal Muscle Leg	muscle
41	chr18:9594400-9597400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr18:9594400-9600000	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr18:9594600-9597000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr18:9594600-9597200	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr18:9594600-9597400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr18:9594800-9597400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr18:9594800-9597400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr18:9594800-9597600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr18:9594800-9597800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr18:9594800-9600200	Weak transcription	Monocytes-CD14+_RO01746	blood

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