Variant report

Variant	rs12644498
Chromosome Location	chr4:57372630-57372631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57372251..57375793-chr4:57396612..57399157,3	K562	blood:
2	chr4:57332191..57334066-chr4:57372574..57375327,2	K562	blood:
3	chr4:57371959..57374819-chr4:57375390..57378214,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174780	Chromatin interaction
ENSG00000249693	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10212643	0.83[EUR][1000 genomes]
rs1140982	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1142851	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11934479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11934636	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940993	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12640212	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12643989	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12649799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650288	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13134963	0.84[JPT][hapmap]
rs1579019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086759	1.00[CEU][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17086773	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086804	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086830	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086860	0.83[YRI][hapmap]
rs17086868	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086909	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176785	0.84[JPT][hapmap]
rs2271924	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34398021	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34419325	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733324	0.81[JPT][hapmap]
rs3733326	0.85[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796539	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796540	1.00[CEU][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796549	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796550	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4076103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4128534	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs41498446	0.81[JPT][hapmap]
rs4631106	0.84[JPT][hapmap]
rs55778537	0.82[ASN][1000 genomes]
rs55903333	0.82[ASN][1000 genomes]
rs55909588	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56129706	0.82[ASN][1000 genomes]
rs56296497	0.82[ASN][1000 genomes]
rs56362514	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57245446	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58654038	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59153415	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59686671	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59764923	0.80[ASN][1000 genomes]
rs59828502	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6830145	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831869	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7437839	0.85[EUR][1000 genomes]
rs7658340	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7688482	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[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	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
5	nsv829941	chr4:57359551-57553136	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12644498	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57370200-57373000	Weak transcription	Dnd41	blood
2	chr4:57370200-57377400	Weak transcription	K562	blood
3	chr4:57371200-57373000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr4:57371200-57373000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr4:57371200-57373000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:57371400-57372800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
7	chr4:57371400-57372800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:57371400-57372800	Flanking Active TSS	Primary B cells from peripheral blood	blood
9	chr4:57371400-57372800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:57371400-57372800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr4:57371400-57372800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr4:57371400-57372800	Active TSS	Brain Angular Gyrus	brain
13	chr4:57371400-57372800	Active TSS	Brain Substantia Nigra	brain
14	chr4:57371400-57372800	Active TSS	Fetal Kidney	kidney
15	chr4:57371400-57372800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
16	chr4:57371400-57372800	Flanking Active TSS	Thymus	Thymus
17	chr4:57371400-57372800	Flanking Active TSS	NHEK	skin
18	chr4:57371400-57373000	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr4:57371400-57373000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:57371400-57373000	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr4:57371400-57373000	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr4:57371400-57373000	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr4:57371400-57373000	Flanking Active TSS	HUVEC	blood vessel
24	chr4:57371400-57373200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:57371600-57372800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr4:57371600-57372800	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr4:57371600-57372800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr4:57371600-57372800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:57371600-57372800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:57371600-57372800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
31	chr4:57371600-57372800	Flanking Active TSS	Gastric	stomach
32	chr4:57371600-57373000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
33	chr4:57371600-57373000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
34	chr4:57371600-57373000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr4:57371600-57373200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:57372000-57372800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr4:57372000-57372800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:57372000-57372800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
39	chr4:57372000-57372800	Flanking Active TSS	Fetal Heart	heart
40	chr4:57372000-57372800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
41	chr4:57372000-57372800	Enhancers	Lung	lung
42	chr4:57372000-57372800	Active TSS	Right Atrium	heart
43	chr4:57372000-57373000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:57372200-57372800	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:57372200-57372800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr4:57372200-57372800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr4:57372200-57372800	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr4:57372200-57372800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr4:57372200-57372800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
50	chr4:57372200-57372800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle

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