Variant report

Variant	rs12508008
Chromosome Location	chr4:57353767-57353768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57328799..57330344-chr4:57353058..57354752,2	K562	blood:
2	chr4:57351584..57356949-chr4:57358180..57362673,6	MCF-7	breast:
3	chr4:57341371..57344122-chr4:57353182..57355439,2	K562	blood:
4	chr4:57344373..57346717-chr4:57352646..57354523,2	MCF-7	breast:
5	chr4:57333275..57335300-chr4:57351105..57353868,3	MCF-7	breast:
6	chr4:57351771..57354637-chr4:57365745..57368105,2	K562	blood:
7	chr4:57345865..57348300-chr4:57353510..57355906,2	K562	blood:
8	chr4:57352661..57355120-chr4:57401191..57403629,2	K562	blood:
9	chr4:57353455..57355932-chr4:57360077..57362846,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000174780	Chromatin interaction
ENSG00000270109	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10008223	0.80[ASN][1000 genomes]
rs10013402	0.82[ASN][1000 genomes]
rs10017460	0.81[ASN][1000 genomes]
rs10051	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10434444	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs10434445	0.80[ASN][1000 genomes]
rs1060472	0.95[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs11133442	0.90[ASW][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs11610	0.84[MEX][hapmap]
rs12498340	0.95[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap]
rs12501334	0.83[ASN][1000 genomes]
rs12503412	0.83[ASN][1000 genomes]
rs12504291	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12505767	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12505939	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12509542	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510712	0.85[ASN][1000 genomes]
rs12511770	0.91[ASN][1000 genomes]
rs12513091	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12646890	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13147900	0.85[JPT][hapmap]
rs1401904	0.85[JPT][hapmap]
rs1401906	0.84[JPT][hapmap]
rs14211	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];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474179	0.92[ASN][1000 genomes]
rs17086696	0.95[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs17086794	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17086832	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086853	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967559	0.90[ASW][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.89[ASN][1000 genomes]
rs1983378	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2030366	0.83[ASN][1000 genomes]
rs28510634	0.80[ASN][1000 genomes]
rs28866881	0.83[ASN][1000 genomes]
rs4340842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4346704	0.91[ASN][1000 genomes]
rs4618376	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864579	0.82[ASN][1000 genomes]
rs4864580	0.82[ASN][1000 genomes]
rs4864583	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4864585	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4865092	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs4865103	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4865107	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4865108	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5010012	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs55915354	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56040009	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56099714	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56229630	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56392224	0.83[ASN][1000 genomes]
rs56887793	0.84[ASN][1000 genomes]
rs58151706	0.82[ASN][1000 genomes]
rs58333131	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6554345	0.85[JPT][hapmap]
rs6554358	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[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];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66858948	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66863699	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6811821	0.80[CEU][hapmap]
rs6820314	0.83[ASN][1000 genomes]
rs6821301	0.84[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6824893	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6829250	0.83[ASN][1000 genomes]
rs6832797	0.81[ASN][1000 genomes]
rs6834696	0.85[ASN][1000 genomes]
rs6834736	0.85[JPT][hapmap]
rs6848187	0.84[MEX][hapmap]
rs6849183	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7664841	0.90[ASW][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];0.94[ASN][1000 genomes]
rs8340	0.95[CHD][hapmap];0.91[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12508008	SRP72	cis	Adipose Subcutaneous	GTEx
rs12508008	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs12508008	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs12508008	SRP72	cis	lymphoblastoid	seeQTL
rs12508008	SRP72	cis	cerebellum	SCAN
rs12508008	SRP72	cis	Esophagus Mucosa	GTEx
rs12508008	SRP72	cis	normal skin	skin_eQTL
rs12508008	SRP72	cis	parietal	SCAN
rs12508008	SRP72	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57334800-57364000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:57334800-57371200	Weak transcription	Stomach Mucosa	stomach
3	chr4:57335000-57354400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:57335200-57371400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:57335600-57370200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr4:57335800-57354800	Weak transcription	Fetal Heart	heart
7	chr4:57335800-57359000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr4:57335800-57365600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:57335800-57369200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:57335800-57370200	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr4:57335800-57370800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:57336000-57362200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:57336000-57362600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:57336000-57364200	Strong transcription	Osteobl	bone
15	chr4:57336000-57369400	Strong transcription	Liver	Liver
16	chr4:57336000-57369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:57336000-57370000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:57336000-57370000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr4:57336000-57370200	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr4:57336000-57371000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:57336200-57365000	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr4:57336200-57369200	Strong transcription	Fetal Thymus	thymus
23	chr4:57336200-57370000	Strong transcription	Placenta	Placenta
24	chr4:57336200-57370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:57336400-57364800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr4:57336400-57365400	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr4:57336400-57368200	Strong transcription	Fetal Muscle Trunk	muscle
28	chr4:57336400-57369200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:57336400-57369200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:57336400-57370200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:57336600-57360400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:57336600-57364200	Strong transcription	Dnd41	blood
33	chr4:57336600-57365400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:57336600-57369200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr4:57337200-57363800	Strong transcription	Duodenum Mucosa	Duodenum
36	chr4:57337200-57365400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr4:57337200-57369200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:57337400-57359000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr4:57337600-57358400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr4:57337600-57364000	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr4:57337600-57364800	Strong transcription	Fetal Intestine Large	intestine
42	chr4:57337800-57358000	Strong transcription	Fetal Lung	lung
43	chr4:57337800-57362400	Strong transcription	Primary B cells from cord blood	blood
44	chr4:57337800-57363200	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr4:57337800-57365600	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr4:57337800-57369200	Strong transcription	Adipose Nuclei	Adipose
47	chr4:57337800-57369400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:57338000-57365000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr4:57338200-57364200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr4:57340600-57366600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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