Variant report

Variant	rs640000
Chromosome Location	chr19:39926601-39926602
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:569)
CpG islands
(count:0)
Chromatin interactive
region (count:43)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:569 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39926073-39927049	Hela-S3	cervix:	n/a	n/a
2	SP2	chr19:39926366-39926865	K562	blood:	n/a	n/a
3	MAX	chr19:39926200-39927085	ECC-1	luminal epithelium:	n/a	n/a
4	ETS1	chr19:39926149-39926947	K562	blood:	n/a	chr19:39926386-39926399 chr19:39926577-39926586 chr19:39926578-39926587
5	GABPA	chr19:39926395-39927120	H1-hESC	embryonic stem cell:	n/a	chr19:39926625-39926634 chr19:39926625-39926636 chr19:39926622-39926636
6	CEBPB	chr19:39926458-39926931	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr19:39926140-39927109	MCF-7	breast:	n/a	n/a
8	CEBPD	chr19:39926383-39927021	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:39926142-39927106	GM19099	blood:	n/a	n/a
10	IRF4	chr19:39926333-39926813	GM12878	blood:	n/a	n/a
11	SIN3AK20	chr19:39926101-39926997	K562	blood:	n/a	n/a
12	STAT3	chr19:39926591-39926876	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr19:39926056-39926698	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr19:39926142-39926960	A549	lung:	n/a	n/a
15	YY1	chr19:39926376-39926809	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr19:39920860-39927633	U87	brain:	n/a	n/a
17	POLR2A	chr19:39926296-39926999	HepG2	liver:	n/a	n/a
18	POLR2A	chr19:39925924-39927273	K562	blood:	n/a	n/a
19	POLR2A	chr19:39925845-39927366	K562	blood:	n/a	n/a
20	POLR2A	chr19:39925936-39927087	HL-60	blood:	n/a	n/a
21	REST	chr19:39926244-39927109	PFSK-1	brain:	n/a	n/a
22	KAP1	chr19:39926421-39926858	U2OS	brain:	n/a	n/a
23	SP1	chr19:39926301-39926945	GM12878	blood:	n/a	chr19:39926456-39926465 chr19:39926689-39926698 chr19:39926687-39926699 chr19:39926455-39926469
24	MAFF	chr19:39926477-39926867	HepG2	liver:	n/a	n/a
25	BHLHE40	chr19:39926489-39927014	GM12878	blood:	n/a	n/a
26	CTCF	chr19:39926480-39926630	BJ	skin:	n/a	n/a
27	POLR2A	chr19:39921036-39927449	GM12878	blood:	n/a	n/a
28	ZC3H11A	chr19:39926384-39926937	K562	blood:	n/a	n/a
29	POLR2A	chr19:39925966-39927022	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr19:39926520-39926670	AG04449	skin:	n/a	n/a
31	POLR2A	chr19:39920920-39927829	PFSK-1	brain:	n/a	n/a
32	REST	chr19:39926265-39927080	HL-60	blood:	n/a	n/a
33	MEF2A	chr19:39926340-39927028	GM12878	blood:	n/a	n/a
34	HCFC1	chr19:39925822-39927487	Hela-S3	cervix:	n/a	n/a
35	ELF1	chr19:39926398-39926944	HepG2	liver:	n/a	n/a
36	TAF7	chr19:39926432-39926639	K562	blood:	n/a	n/a
37	MXI1	chr19:39926209-39927021	Hela-S3	cervix:	n/a	n/a
38	SIN3AK20	chr19:39926174-39926688	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr19:39926047-39927184	K562	blood:	n/a	n/a
40	TAF1	chr19:39926182-39927042	Hela-S3	cervix:	n/a	n/a
41	E2F6	chr19:39926513-39926990	K562	blood:	n/a	chr19:39926626-39926635
42	CTCF	chr19:39926520-39926670	HA-sp	spinal cord:	n/a	n/a
43	MBD4	chr19:39926237-39926748	HepG2	liver:	n/a	n/a
44	SIN3AK20	chr19:39926382-39926936	PFSK-1	brain:	n/a	n/a
45	POLR2A	chr19:39925995-39927420	K562	blood:	n/a	n/a
46	MAX	chr19:39926214-39926988	HepG2	liver:	n/a	n/a
47	ETS1	chr19:39926313-39926988	GM12878	blood:	n/a	chr19:39926386-39926399 chr19:39926577-39926586 chr19:39926578-39926587
48	CEBPB	chr19:39926230-39927166	GM12878	blood:	n/a	n/a
49	NR2F2	chr19:39926019-39927095	K562	blood:	n/a	n/a
50	POLR2A	chr19:39926031-39927050	GM12892	blood:	n/a	n/a

No data

(count:43 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39926370..39927938-chr19:40004340..40006529,2	K562	blood:
2	chr19:39832709..39837239-chr19:39925090..39928725,4	K562	blood:
3	chr1:44440402..44441005-chr19:39926600..39927279,2	HCT-116	colon:
4	chr19:39925083..39926660-chr19:39982191..39985073,2	K562	blood:
5	chr19:39926041..39928299-chr19:40334872..40337810,2	MCF-7	breast:
6	chr19:39925979..39927964-chr19:39971323..39973932,2	K562	blood:
7	chr1:16154241..16155259-chr19:39926092..39927110,8	HCT-116	colon:
8	chr19:39926474..39927082-chr9:139622216..139623108,2	HCT-116	colon:
9	chr19:39926154..39926654-chr3:169482327..169483268,2	Hela-S3	cervix:
10	chr19:39926340..39927030-chr6:7390001..7390598,2	HCT-116	colon:
11	chr19:39926454..39927410-chr19:49121867..49122447,2	NB4	blood:
12	chr17:74722749..74723468-chr19:39926405..39927013,2	Hela-S3	cervix:
13	chr10:112257511..112258462-chr19:39926345..39927316,2	Hela-S3	cervix:
14	chr19:39924275..39926732-chr19:39958030..39960191,3	K562	blood:
15	chr19:39926302..39926892-chr5:73980939..73981515,2	Hela-S3	cervix:
16	chr10:121301884..121302498-chr19:39926232..39927047,2	HCT-116	colon:
17	chr19:39903704..39904525-chr19:39926143..39926832,3	MCF-7	breast:
18	chr12:122230934..122231621-chr19:39926580..39927261,2	Hela-S3	cervix:
19	chr11:65266485..65267920-chr19:39926109..39927040,4	Hela-S3	cervix:
20	chr14:20937139..20937928-chr19:39926131..39927013,2	Hela-S3	cervix:
21	chr19:39925003..39927867-chr19:40028857..40032200,4	K562	blood:
22	chr19:39926523..39927127-chr6:35436191..35436721,2	HCT-116	colon:
23	chr11:63952709..63953353-chr19:39926267..39927257,2	HCT-116	colon:
24	chr19:39875302..39877706-chr19:39923653..39926638,3	MCF-7	breast:
25	chr19:39925059..39926909-chr6:27114877..27117589,2	MCF-7	breast:
26	chr19:39926419..39927362-chr20:46130010..46130813,2	NB4	blood:
27	chr19:39923160..39926894-chr19:40022027..40025011,8	K562	blood:
28	chr19:39925068..39927999-chr19:40329043..40331985,2	K562	blood:
29	chr19:39832183..39834517-chr19:39925160..39926923,2	MCF-7	breast:
30	chr19:39925314..39927864-chr19:40336547..40338108,2	K562	blood:
31	chr19:39924469..39929022-chr19:39934307..39938518,21	MCF-7	breast:
32	chr10:21814455..21814982-chr19:39926443..39927093,2	HCT-116	colon:
33	chr19:39923771..39928393-chr19:40029138..40032183,4	MCF-7	breast:
34	chr19:39925899..39926885-chr6:32939557..32940381,2	Hela-S3	cervix:
35	chr19:39926269..39927245-chr9:116138857..116139630,2	HCT-116	colon:
36	chr19:39926032..39928483-chr19:40324303..40326455,2	MCF-7	breast:
37	chr19:39926030..39926817-chr5:176924186..176924945,2	Hela-S3	cervix:
38	chr19:39925768..39926759-chr7:26240090..26240786,2	Hela-S3	cervix:
39	chr19:39924549..39928313-chr19:39970394..39973544,4	MCF-7	breast:
40	chr19:39925083..39928891-chr19:40028576..40030872,3	K562	blood:
41	chr19:39923294..39928217-chr19:39969939..39976745,7	K562	blood:
42	chr19:39925075..39926642-chr19:40022135..40025107,3	K562	blood:
43	chr10:14645782..14646722-chr19:39926153..39926683,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
RPS16	TF binding region
ENSG00000213922	TF binding region
SUPT5H	TF binding region
ENSG00000122565	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000270141	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000065809	Chromatin interaction
ENSG00000070495	Chromatin interaction
ENSG00000006712	Chromatin interaction
ENSG00000198805	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000198755	Chromatin interaction
ENSG00000105204	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000168439	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000196923	Chromatin interaction
ENSG00000124151	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000049860	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000138166	Chromatin interaction
ENSG00000233016	Chromatin interaction
ENSG00000180592	Chromatin interaction
ENSG00000181038	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000119431	Chromatin interaction
ENSG00000122566	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000105202	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000117410	Chromatin interaction
ENSG00000178715	Chromatin interaction
ENSG00000063177	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000269792	Chromatin interaction
ENSG00000186838	Chromatin interaction
ENSG00000148908	Chromatin interaction
ENSG00000124784	Chromatin interaction
ENSG00000269584	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1130180	0.81[ASN][1000 genomes]
rs11881477	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12978920	0.83[ASN][1000 genomes]
rs1529732	0.81[ASN][1000 genomes]
rs17626	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865091	0.87[ASN][1000 genomes]
rs1865092	0.83[ASN][1000 genomes]
rs1932	0.84[ASN][1000 genomes]
rs2116932	0.84[ASN][1000 genomes]
rs2353678	0.87[ASN][1000 genomes]
rs2353679	0.86[ASN][1000 genomes]
rs251855	0.87[ASN][1000 genomes]
rs251856	0.89[ASN][1000 genomes]
rs251857	0.89[ASN][1000 genomes]
rs251858	0.89[ASN][1000 genomes]
rs251859	0.88[ASN][1000 genomes]
rs251860	0.85[ASN][1000 genomes]
rs28528765	0.83[ASN][1000 genomes]
rs28649498	0.82[ASN][1000 genomes]
rs4390710	0.87[ASN][1000 genomes]
rs4802026	0.83[ASN][1000 genomes]
rs4803237	0.81[ASN][1000 genomes]
rs480595	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480656	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs481421	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504017	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs530411	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs566130	0.91[ASN][1000 genomes]
rs6508862	0.84[ASN][1000 genomes]
rs651601	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs686956	0.89[ASN][1000 genomes]
rs7255253	0.81[ASN][1000 genomes]
rs73035416	0.81[ASN][1000 genomes]
rs73549933	0.81[ASN][1000 genomes]
rs8107194	0.81[ASN][1000 genomes]
rs8107647	0.81[ASN][1000 genomes]
rs8110134	0.85[ASN][1000 genomes]
rs8110716	0.85[ASN][1000 genomes]
rs878754	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
3	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS 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	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs640000	ENSG00000105193	cis	multi-tissue	Pritchard
rs640000	RPS16	Cis_1M	lymphoblastoid	RTeQTL
rs640000	LOC441876///RPS16	Cis_1M	lymphoblastoid	RTeQTL
rs640000	RPS16	cis	Heart Left Ventricle	GTEx
rs640000	RPS16	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39925000-39927200	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr19:39925200-39927000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr19:39925200-39927400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr19:39925400-39927000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:39925400-39927000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr19:39925400-39927200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr19:39925400-39927200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr19:39925400-39927200	Active TSS	Psoas Muscle	Psoas
9	chr19:39925400-39927200	Active TSS	Right Ventricle	heart
10	chr19:39925400-39927400	Active TSS	H9 Cell Line	embryonic stem cell
11	chr19:39925400-39927600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:39925400-39927600	Active TSS	GM12878-XiMat	blood
13	chr19:39925600-39927000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr19:39925600-39927000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:39925600-39927000	Active TSS	Fetal Kidney	kidney
16	chr19:39925600-39927000	Active TSS	Hela-S3	cervix
17	chr19:39925600-39927000	Active TSS	NHDF-Ad	bronchial
18	chr19:39925600-39927200	Active TSS	HMEC	breast
19	chr19:39925600-39927400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:39925600-39927400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr19:39925600-39927400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr19:39925600-39927400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr19:39925600-39927600	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr19:39925600-39927800	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr19:39925800-39926800	Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr19:39925800-39926800	Active TSS	Fetal Thymus	thymus
27	chr19:39925800-39926800	Active TSS	Thymus	Thymus
28	chr19:39925800-39926800	Active TSS	HSMM	muscle
29	chr19:39925800-39926800	Active TSS	NH-A	brain
30	chr19:39925800-39927000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:39925800-39927000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:39925800-39927000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr19:39925800-39927000	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr19:39925800-39927000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr19:39925800-39927000	Active TSS	Muscle Satellite Cultured Cells	--
36	chr19:39925800-39927000	Active TSS	Brain Angular Gyrus	brain
37	chr19:39925800-39927000	Active TSS	Brain Hippocampus Middle	brain
38	chr19:39925800-39927000	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr19:39925800-39927000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:39925800-39927000	Active TSS	Colon Smooth Muscle	Colon
41	chr19:39925800-39927000	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr19:39925800-39927000	Active TSS	Fetal Heart	heart
43	chr19:39925800-39927000	Active TSS	Fetal Intestine Large	intestine
44	chr19:39925800-39927000	Active TSS	Fetal Intestine Small	intestine
45	chr19:39925800-39927000	Active TSS	Fetal Lung	lung
46	chr19:39925800-39927000	Active TSS	Rectal Smooth Muscle	rectum
47	chr19:39925800-39927000	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr19:39925800-39927000	Active TSS	Stomach Mucosa	stomach
49	chr19:39925800-39927000	Active TSS	K562	blood
50	chr19:39925800-39927000	Active TSS	NHLF	lung

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