Variant report

Variant	rs2510785
Chromosome Location	chr4:95444407-95444408
allele	A/C
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	CEBPB	chr4:95444329-95444835	A549	lung:	n/a	chr4:95444599-95444608 chr4:95444599-95444610 chr4:95444597-95444608
2	SPI1	chr4:95444229-95444471	GM12878	blood:	n/a	n/a
3	SPI1	chr4:95444305-95444455	GM12878	blood:	n/a	n/a
4	TBL1XR1	chr4:95444403-95444496	K562	blood:	n/a	n/a
5	FOS	chr4:95444314-95445144	HUVEC	blood vessel:	n/a	chr4:95445088-95445100 chr4:95445090-95445098 chr4:95444957-95444968 chr4:95445091-95445102

Variant related genes	Relation type
PDLIM5	TF binding region

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];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2433317	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]
rs2433324	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.98[ASN][1000 genomes]
rs2433325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2438142	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2438143	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2438144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452554	0.91[GIH][hapmap];0.83[MEX][hapmap]
rs2452559	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2452560	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2452561	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2452562	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2452564	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2452565	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2452566	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2452568	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510778	0.94[CEU][hapmap]
rs2510786	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510787	0.91[CEU][hapmap]
rs2510788	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]
rs2510791	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2510792	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2510794	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2510795	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]
rs2510802	0.80[CHD][hapmap];0.91[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
rs2510785	RAP1GDS1	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95422400-95482800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:95430000-95456200	Weak transcription	Small Intestine	intestine
3	chr4:95435800-95444600	Enhancers	Fetal Heart	heart
4	chr4:95436400-95447200	Enhancers	Colon Smooth Muscle	Colon
5	chr4:95436800-95447800	Weak transcription	Fetal Intestine Small	intestine
6	chr4:95437200-95448400	Weak transcription	HSMM	muscle
7	chr4:95437400-95445000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:95437600-95456000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:95437800-95448600	Weak transcription	NHEK	skin
10	chr4:95438000-95448400	Weak transcription	Fetal Intestine Large	intestine
11	chr4:95438200-95448800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:95438200-95454600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:95438400-95454800	Weak transcription	Hela-S3	cervix
14	chr4:95438600-95445000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:95438800-95446800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:95438800-95448600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:95439000-95447000	Weak transcription	HepG2	liver
18	chr4:95439400-95448800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:95439800-95444600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr4:95440400-95444800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:95440400-95446200	Weak transcription	Ovary	ovary
22	chr4:95440400-95447000	Weak transcription	Fetal Lung	lung
23	chr4:95440400-95448400	Weak transcription	Brain Substantia Nigra	brain
24	chr4:95440400-95455000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:95440600-95447200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr4:95440600-95448400	Weak transcription	Aorta	Aorta
27	chr4:95440600-95448800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:95440600-95449000	Weak transcription	Fetal Muscle Leg	muscle
29	chr4:95440600-95449000	Weak transcription	Pancreas	Pancrea
30	chr4:95440600-95454200	Weak transcription	Fetal Stomach	stomach
31	chr4:95440600-95454600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr4:95440600-95454800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:95440600-95456200	Weak transcription	Spleen	Spleen
34	chr4:95440600-95456400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:95440600-95456600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:95440800-95446800	Weak transcription	Stomach Mucosa	stomach
37	chr4:95440800-95454200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr4:95441000-95451800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr4:95441200-95445600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:95441400-95455000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr4:95441600-95447800	Weak transcription	Placenta	Placenta
42	chr4:95441600-95451400	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr4:95441600-95454600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr4:95441800-95445600	Weak transcription	Brain Anterior Caudate	brain
45	chr4:95442000-95469600	Weak transcription	Primary T cells from cord blood	blood
46	chr4:95442200-95447400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:95442600-95447400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr4:95442600-95448600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:95442600-95455200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:95443000-95445000	Enhancers	Rectal Smooth Muscle	rectum

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