Variant report

Variant	rs2510788
Chromosome Location	chr4:95438406-95438407
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95371867..95374212-chr4:95437393..95439131,2	K562	blood:

Variant related genes	Relation type
ENSG00000163110	Chromatin interaction
ENSG00000203436	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1353044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2433317	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]
rs2433324	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2433325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2438142	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];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2438143	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2438144	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];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452554	0.87[GIH][hapmap]
rs2452559	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2452560	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2452561	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2452562	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2452564	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2452565	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2452566	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2452568	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510778	0.94[CEU][hapmap]
rs2510785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510786	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510787	0.92[CEU][hapmap]
rs2510791	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2510792	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2510794	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2510795	0.94[CEU][hapmap];0.87[CHB][hapmap];0.91[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]
rs2510802	0.81[CHD][hapmap];0.83[MEX][hapmap]
rs2577056	0.94[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
rs2510788	RAP1GDS1	cis	parietal	SCAN

Chromatin state (count:61 , 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	chr4:95415400-95440200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr4:95421200-95440000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:95421600-95440000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr4:95422400-95482800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:95429800-95440000	Weak transcription	Esophagus	oesophagus
8	chr4:95429800-95440000	Weak transcription	Ovary	ovary
9	chr4:95430000-95456200	Weak transcription	Small Intestine	intestine
10	chr4:95430600-95440000	Weak transcription	Right Ventricle	heart
11	chr4:95430600-95444000	Weak transcription	HSMMtube	muscle
12	chr4:95431200-95440000	Weak transcription	Pancreas	Pancrea
13	chr4:95431400-95438600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:95435600-95440000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr4:95435800-95440200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr4:95435800-95444600	Enhancers	Fetal Heart	heart
17	chr4:95436200-95439200	Enhancers	NH-A	brain
18	chr4:95436200-95439400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr4:95436200-95439400	Enhancers	Rectal Smooth Muscle	rectum
20	chr4:95436200-95441600	Enhancers	Liver	Liver
21	chr4:95436400-95440000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr4:95436400-95447200	Enhancers	Colon Smooth Muscle	Colon
23	chr4:95436600-95439000	Enhancers	HepG2	liver
24	chr4:95436600-95439600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr4:95436800-95438800	Enhancers	NHLF	lung
26	chr4:95436800-95447800	Weak transcription	Fetal Intestine Small	intestine
27	chr4:95437000-95438600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:95437200-95438800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:95437200-95438800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:95437200-95438800	Enhancers	HMEC	breast
31	chr4:95437200-95448400	Weak transcription	HSMM	muscle
32	chr4:95437400-95438800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:95437400-95439200	Enhancers	K562	blood
34	chr4:95437400-95440000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr4:95437400-95445000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:95437600-95438600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr4:95437600-95440000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:95437600-95441000	Enhancers	A549	lung
39	chr4:95437600-95456000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr4:95437800-95440000	Weak transcription	Right Atrium	heart
41	chr4:95437800-95440000	Enhancers	HUVEC	blood vessel
42	chr4:95437800-95440400	Enhancers	Osteobl	bone
43	chr4:95437800-95441200	Weak transcription	NHDF-Ad	bronchial
44	chr4:95437800-95448600	Weak transcription	NHEK	skin
45	chr4:95438000-95438800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:95438000-95439800	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr4:95438000-95439800	Weak transcription	Placenta	Placenta
48	chr4:95438000-95440000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:95438000-95440000	Weak transcription	Aorta	Aorta
50	chr4:95438000-95440000	Weak transcription	Left Ventricle	heart

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