Variant report

Variant	rs2433317
Chromosome Location	chr4:95428800-95428801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95427467..95429085-chr4:95430722..95432306,2	K562	blood:
2	chr4:95372282..95374578-chr4:95428337..95431259,2	K562	blood:
3	chr4:95372028..95373617-chr4:95427341..95430036,2	MCF-7	breast:
4	chr4:95372296..95374586-chr4:95428181..95430528,2	MCF-7	breast:
5	chr4:95371846..95374578-chr4:95428736..95431275,4	K562	blood:

Variant related genes	Relation type
ENSG00000163110	Chromatin interaction
ENSG00000203436	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1353044	0.94[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2433318	0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs2433324	0.84[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs2433325	0.94[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2438141	0.85[ASN][1000 genomes]
rs2438142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2438143	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2438144	0.94[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2438145	0.90[ASN][1000 genomes]
rs2452554	0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs2452556	0.88[ASN][1000 genomes]
rs2452557	0.88[ASN][1000 genomes]
rs2452558	0.90[ASN][1000 genomes]
rs2452559	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452560	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452561	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2452562	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452564	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452565	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452566	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2452568	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2510778	0.89[CEU][hapmap]
rs2510785	0.82[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2510786	0.94[CEU][hapmap];0.80[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2510787	0.84[CEU][hapmap]
rs2510788	0.94[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2510791	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2510792	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510794	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510795	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510798	0.90[ASN][1000 genomes]
rs2510799	0.88[ASN][1000 genomes]
rs2510800	0.85[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs2510801	0.86[ASN][1000 genomes]
rs2510802	0.86[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs2510803	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2510804	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2577056	0.89[CEU][hapmap]

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	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv594901	chr4:95254730-95493246	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1003743	chr4:95255957-95469831	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2433317	RAP1GDS1	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95375000-95440200	Weak transcription	Primary T cells from cord blood	blood
2	chr4:95400800-95440000	Weak transcription	Lung	lung
3	chr4:95405000-95429000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:95414600-95429000	Weak transcription	Esophagus	oesophagus
5	chr4:95415400-95429000	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:95415400-95440200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr4:95418000-95430800	Weak transcription	Pancreas	Pancrea
8	chr4:95421200-95429000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:95421200-95429600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:95421200-95440000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:95421400-95431400	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr4:95421600-95440000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr4:95422400-95429000	Weak transcription	Ovary	ovary
14	chr4:95422400-95482800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr4:95423200-95436600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:95424000-95429200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:95424600-95431800	Enhancers	Colon Smooth Muscle	Colon
18	chr4:95424800-95429200	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr4:95425600-95429800	Enhancers	Psoas Muscle	Psoas
20	chr4:95425800-95428800	Enhancers	Fetal Heart	heart
21	chr4:95425800-95429000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:95426200-95428800	Enhancers	Stomach Smooth Muscle	stomach
23	chr4:95426400-95429000	Weak transcription	HSMMtube	muscle
24	chr4:95426600-95428800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:95427000-95428800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:95427000-95430600	Enhancers	Liver	Liver
27	chr4:95427200-95429000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:95427200-95429600	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr4:95427400-95430400	Enhancers	Fetal Intestine Large	intestine
30	chr4:95427600-95429400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:95427600-95429800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:95427600-95430400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:95427800-95429600	Genic enhancers	NHEK	skin
34	chr4:95427800-95429800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:95427800-95430200	Enhancers	HepG2	liver
36	chr4:95427800-95430400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr4:95427800-95430400	Enhancers	HMEC	breast
38	chr4:95427800-95430600	Enhancers	Osteobl	bone
39	chr4:95427800-95431400	Enhancers	Duodenum Mucosa	Duodenum
40	chr4:95428000-95428800	Enhancers	GM12878-XiMat	blood
41	chr4:95428000-95429200	Enhancers	Placenta	Placenta
42	chr4:95428000-95429400	Enhancers	HSMM	muscle
43	chr4:95428000-95429800	Enhancers	Gastric	stomach
44	chr4:95428000-95429800	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr4:95428000-95430000	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr4:95428000-95430200	Enhancers	K562	blood
47	chr4:95428000-95430400	Enhancers	NH-A	brain
48	chr4:95428000-95430600	Enhancers	Hela-S3	cervix
49	chr4:95428000-95430800	Enhancers	Muscle Satellite Cultured Cells	--
50	chr4:95428200-95428800	Weak transcription	Fetal Stomach	stomach

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