Variant report

Variant	rs4146259
Chromosome Location	chr2:153363414-153363415
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	chr2:153361979..153364845-chr2:153366999..153370828,3	K562	blood:
2	chr2:153362103..153364845-chr2:153366999..153369468,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10173899	0.94[JPT][hapmap]
rs10179418	0.85[CHD][hapmap];0.88[JPT][hapmap]
rs10194603	0.94[JPT][hapmap]
rs10208776	0.94[JPT][hapmap]
rs10432493	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12617686	0.85[CEU][hapmap]
rs12693378	0.89[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs13390698	0.86[JPT][hapmap]
rs13424038	0.94[JPT][hapmap]
rs13427076	0.88[JPT][hapmap]
rs13427990	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16831169	0.94[JPT][hapmap]
rs16831174	0.94[JPT][hapmap]
rs2346205	0.94[JPT][hapmap]
rs2346209	0.94[JPT][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes]
rs2881336	0.85[CEU][hapmap]
rs2881339	0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs4143274	0.94[JPT][hapmap]
rs4664112	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4664587	0.83[CEU][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs6434059	0.94[CEU][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs6434060	0.82[EUR][1000 genomes]
rs6434061	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6434062	0.82[EUR][1000 genomes]
rs6725661	0.94[JPT][hapmap]
rs6736639	0.84[CEU][hapmap]
rs6737699	0.88[JPT][hapmap]
rs6747765	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs6748954	0.94[JPT][hapmap]
rs7559217	0.94[JPT][hapmap]
rs7582984	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs7586195	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs7587794	0.94[JPT][hapmap]
rs7590079	0.82[CEU][hapmap]
rs7590207	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7592283	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7606592	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[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	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2754362	chr2:153297577-153366129	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4146259	PRPF40A	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153348800-153370200	Weak transcription	Aorta	Aorta
2	chr2:153354600-153364600	Weak transcription	Left Ventricle	heart
3	chr2:153354600-153365200	Weak transcription	Pancreas	Pancrea
4	chr2:153356000-153364600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:153356800-153364600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:153356800-153365000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:153357000-153364800	Weak transcription	Fetal Lung	lung
8	chr2:153357200-153365000	Weak transcription	Fetal Stomach	stomach
9	chr2:153357400-153364600	Weak transcription	Psoas Muscle	Psoas
10	chr2:153357400-153375200	Weak transcription	Right Atrium	heart
11	chr2:153357600-153365000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:153357600-153365200	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:153358200-153364600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:153358200-153365000	Weak transcription	Fetal Brain Female	brain
15	chr2:153359600-153364200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:153360400-153365000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:153360600-153364200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:153360800-153365600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr2:153361000-153364600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:153361000-153365600	Enhancers	Osteobl	bone
21	chr2:153361000-153365800	Enhancers	NH-A	brain
22	chr2:153361000-153398600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:153361200-153365400	Flanking Active TSS	A549	lung
24	chr2:153361200-153365600	Enhancers	HMEC	breast
25	chr2:153361200-153365600	Enhancers	HUVEC	blood vessel
26	chr2:153361200-153365800	Enhancers	Brain Hippocampus Middle	brain
27	chr2:153361400-153364000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:153361400-153364400	Weak transcription	NHLF	lung
29	chr2:153361600-153369800	Weak transcription	NHDF-Ad	bronchial
30	chr2:153361800-153365600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:153362000-153365600	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr2:153362400-153363600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:153362400-153364600	Weak transcription	Fetal Heart	heart
34	chr2:153362400-153364600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:153362400-153364600	Weak transcription	HSMM	muscle
36	chr2:153362400-153364800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:153362400-153364800	Weak transcription	HSMMtube	muscle
38	chr2:153362400-153365000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:153362400-153365200	Weak transcription	Ovary	ovary
40	chr2:153362400-153379400	Weak transcription	Fetal Brain Male	brain
41	chr2:153362600-153363600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr2:153362600-153364400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:153362600-153364600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:153362600-153364800	Weak transcription	Brain Anterior Caudate	brain
45	chr2:153362600-153365600	Enhancers	Brain Substantia Nigra	brain
46	chr2:153362800-153363600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:153362800-153364000	Flanking Active TSS	GM12878-XiMat	blood
48	chr2:153362800-153365000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:153363000-153364000	Enhancers	Small Intestine	intestine
50	chr2:153363200-153363600	Enhancers	Fetal Kidney	kidney

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