Variant report

Variant	rs7437839
Chromosome Location	chr4:57257341-57257342
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:57256625-57257341	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr4:57257201-57257415	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:57255602-57258077	GM12892	blood:	n/a	n/a
4	POLR2A	chr4:57257313-57257420	K562	blood:	n/a	n/a
5	POLR2A	chr4:57253107-57259459	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57256134..57259107-chr4:57259816..57262815,2	MCF-7	breast:
2	chr4:57255720..57258626-chr4:57264661..57268559,4	K562	blood:
3	chr4:57255304..57257966-chr4:57332773..57334646,2	MCF-7	breast:
4	chr4:57256994..57259922-chr4:57269239..57271312,2	K562	blood:
5	chr4:57256866..57258507-chr4:57276793..57279015,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAICS-3	chr4:57253640-57259528	NONHSAT096500

No data

Variant related genes	Relation type
AASDH	TF binding region
ENSG00000174780	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000270147	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1140982	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1142851	0.85[EUR][1000 genomes]
rs11934479	0.85[EUR][1000 genomes]
rs11934636	0.85[EUR][1000 genomes]
rs11940993	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12640212	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12643989	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12643996	0.85[EUR][1000 genomes]
rs12644498	0.85[EUR][1000 genomes]
rs12649799	0.85[EUR][1000 genomes]
rs12650288	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1579019	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17086759	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086773	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17086801	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17086804	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17086830	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17086838	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17086868	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17086898	0.85[EUR][1000 genomes]
rs17086909	0.85[EUR][1000 genomes]
rs17086919	0.85[EUR][1000 genomes]
rs17086922	0.85[EUR][1000 genomes]
rs2271924	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34398021	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34419325	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3733324	0.95[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3733326	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796539	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796540	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796549	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796550	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4076103	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41498446	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs55778537	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55890437	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55903333	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55909588	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56095772	0.95[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs56129706	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56296497	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56362514	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56406704	0.91[ASN][1000 genomes]
rs57233429	1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs57245446	0.85[EUR][1000 genomes]
rs58654038	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59062367	1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs59153415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59278715	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs59764923	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59828502	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6830145	0.85[EUR][1000 genomes]
rs6831869	0.85[EUR][1000 genomes]
rs7688482	0.92[EUR][1000 genomes];0.82[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	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	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
5	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7437839	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254200-57273800	Weak transcription	Spleen	Spleen
2	chr4:57254400-57268400	Weak transcription	Lung	lung
3	chr4:57254400-57273600	Weak transcription	Pancreas	Pancrea
4	chr4:57254600-57264000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:57254600-57271600	Weak transcription	Ovary	ovary
6	chr4:57254600-57276400	Weak transcription	Psoas Muscle	Psoas
7	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:57254800-57260800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:57254800-57261800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:57254800-57262000	Weak transcription	Placenta	Placenta
11	chr4:57254800-57264000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:57254800-57264000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:57254800-57271600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:57254800-57273200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:57254800-57275200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:57254800-57275400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:57254800-57276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:57254800-57276400	Weak transcription	Right Ventricle	heart
19	chr4:57254800-57276600	Weak transcription	Left Ventricle	heart
20	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:57255000-57257800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr4:57255000-57260400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:57255000-57261200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr4:57255000-57262200	Weak transcription	A549	lung
25	chr4:57255000-57264400	Weak transcription	Brain Germinal Matrix	brain
26	chr4:57255000-57264800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr4:57255000-57265600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr4:57255000-57266000	Weak transcription	Primary B cells from cord blood	blood
29	chr4:57255000-57266200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:57255000-57266200	Weak transcription	NH-A	brain
31	chr4:57255000-57266400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr4:57255000-57266400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:57255000-57266600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr4:57255000-57266600	Weak transcription	HSMM	muscle
35	chr4:57255000-57266800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:57255000-57269200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr4:57255000-57271400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr4:57255200-57257800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr4:57255200-57257800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr4:57255200-57257800	Weak transcription	Brain Angular Gyrus	brain
41	chr4:57255200-57258400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:57255200-57259000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr4:57255200-57262000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr4:57255200-57262200	Weak transcription	Fetal Lung	lung
45	chr4:57255200-57262200	Weak transcription	Osteobl	bone
46	chr4:57255200-57264000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr4:57255200-57264000	Weak transcription	Fetal Stomach	stomach
48	chr4:57255200-57266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:57255200-57266200	Weak transcription	HUVEC	blood vessel
50	chr4:57255200-57266400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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