Variant report

Variant	rs12648778
Chromosome Location	chr4:119621293-119621294
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:119620862..119622928-chr4:119629696..119632025,2	K562	blood:
2	chr4:119612053..119615393-chr4:119619067..119621438,3	K562	blood:
3	chr4:119609732..119613553-chr4:119618798..119622906,4	K562	blood:
4	chr4:119608875..119611520-chr4:119620589..119622906,3	K562	blood:

Variant related genes	Relation type
ENSG00000145388	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10022024	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11724866	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11730728	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs11735989	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs11945703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12640223	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12646268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12646298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12648682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13105145	0.83[EUR][1000 genomes]
rs13105732	0.82[EUR][1000 genomes]
rs13111664	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13115157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13124091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13146440	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13146816	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13150663	0.87[EUR][1000 genomes]
rs2029399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2046779	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2288307	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs3087958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34091082	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34270389	0.85[EUR][1000 genomes]
rs34508500	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34628947	0.85[EUR][1000 genomes]
rs35023705	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35071348	0.85[EUR][1000 genomes]
rs35392662	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35404779	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35522890	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35613641	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35952841	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36023173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733517	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66500248	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66942289	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67151421	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67989872	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6813357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817790	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6818241	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6821350	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827740	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs6828070	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6829010	0.85[EUR][1000 genomes]
rs6831197	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6836005	0.94[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6837652	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6847706	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6849714	0.82[EUR][1000 genomes]
rs6852706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6853722	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs6855919	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6857285	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71610228	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72679004	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72679023	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7653962	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7656990	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7662650	0.84[EUR][1000 genomes]
rs7669896	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7681835	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs7692721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7695602	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7696543	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv427693	chr4:119493919-119674742	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12648778	RP11-384K6.6	cis	Artery Tibial	GTEx
rs12648778	KIAA1627	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119607000-119644800	Weak transcription	Small Intestine	intestine
2	chr4:119607200-119659200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:119607800-119625600	Weak transcription	Aorta	Aorta
4	chr4:119607800-119693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:119608000-119645000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:119608600-119635200	Strong transcription	Fetal Thymus	thymus
7	chr4:119608600-119635800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:119608600-119674000	Weak transcription	Stomach Mucosa	stomach
9	chr4:119608800-119625400	Weak transcription	HSMMtube	muscle
10	chr4:119608800-119635000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:119609000-119622600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:119609000-119628200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:119609000-119633200	Strong transcription	Placenta	Placenta
14	chr4:119609000-119633400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:119609000-119633400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:119609000-119633800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:119609000-119634400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:119609000-119634800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr4:119609000-119635000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr4:119609000-119635000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr4:119609000-119636000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:119609000-119636200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr4:119609200-119623400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr4:119609200-119633400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:119609200-119634400	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr4:119609200-119634800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr4:119609200-119635600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:119609200-119635600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:119609200-119635800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr4:119609200-119636200	Strong transcription	Adipose Nuclei	Adipose
31	chr4:119609200-119648600	Weak transcription	Fetal Heart	heart
32	chr4:119609400-119622800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:119609400-119633400	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr4:119609400-119635600	Strong transcription	Dnd41	blood
35	chr4:119610200-119628000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:119610400-119628400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:119610400-119628600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:119611600-119625400	Weak transcription	Ovary	ovary
39	chr4:119611600-119625600	Weak transcription	Fetal Brain Male	brain
40	chr4:119611800-119625600	Weak transcription	Lung	lung
41	chr4:119611800-119625600	Weak transcription	Pancreas	Pancrea
42	chr4:119612000-119628000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:119612800-119624400	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr4:119613000-119622600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr4:119613000-119634400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr4:119613800-119623200	Strong transcription	Brain Germinal Matrix	brain
47	chr4:119614000-119627000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:119614200-119625400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr4:119614200-119625800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr4:119614400-119625400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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