Variant report

Variant	rs530411
Chromosome Location	chr19:39927540-39927541
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:61)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39920860-39927633	U87	brain:	n/a	n/a
2	POLR2A	chr19:39920920-39927829	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr19:39921168-39927547	K562	blood:	n/a	n/a
4	MXI1	chr19:39925603-39927602	SK-N-SH	brain:	n/a	n/a
5	CHD1	chr19:39922434-39927571	IMR90	lung:	n/a	chr19:39927410-39927420
6	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr19:39921043-39927658	HCT-116	colon:	n/a	n/a
8	MYC	chr19:39924499-39927878	A549	lung:	n/a	n/a
9	SIX5	chr19:39920908-39927672	A549	lung:	n/a	chr19:39927463-39927477
10	POLR2A	chr19:39925586-39928296	HepG2	liver:	n/a	n/a
11	STAT3	chr19:39927084-39927565	MCF10A-Er-Src	breast:	n/a	chr19:39927363-39927374 chr19:39927300-39927308 chr19:39927399-39927410 chr19:39927174-39927182 chr19:39927381-39927392
12	STAT3	chr19:39927127-39927565	MCF10A-Er-Src	breast:	n/a	chr19:39927363-39927374 chr19:39927300-39927308 chr19:39927399-39927410 chr19:39927174-39927182 chr19:39927381-39927392
13	PBX3	chr19:39925853-39927596	A549	lung:	n/a	n/a
14	SIN3AK20	chr19:39920798-39927887	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr19:39886449-39939600	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr19:39927373-39927680	MCF-7	breast:	n/a	n/a
17	REST	chr19:39926008-39927640	H1-neurons	neurons:	n/a	n/a
18	POLR2A	chr19:39920886-39928028	SK-N-MC	brain:	n/a	n/a
19	MTA3	chr19:39925925-39927554	GM12878	blood:	n/a	n/a
20	REST	chr19:39925510-39927924	PANC-1	pancreas:	n/a	n/a
21	GABPA	chr19:39925870-39927633	A549	lung:	n/a	chr19:39926625-39926634 chr19:39926625-39926636 chr19:39926622-39926636
22	POLR2A	chr19:39925855-39927641	HCT-116	colon:	n/a	n/a
23	SIN3AK20	chr19:39913141-39929158	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr19:39920881-39927680	U87	brain:	n/a	n/a
25	POLR2A	chr19:39926199-39927621	HCT-116	colon:	n/a	n/a
26	POLR2A	chr19:39925920-39927698	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:39927495-39927545	SK-N-MC	brain:	n/a
2	chr19:39927495-39927545	HNPCEpiC	eye:	n/a
3	chr19:39927495-39927545	HMEC	breast:	n/a
4	chr19:39927495-39927545	HL-60	blood:	n/a
5	chr19:39927495-39927545	GM06990	blood:	n/a
6	chr19:39927495-39927545	GM12891	blood:	n/a
7	chr19:39927495-39927545	SKMC	muscle:	n/a
8	chr19:39927495-39927545	MCF10A-Er-Src	breast:	n/a
9	chr19:39927495-39927545	CMK	blood:	n/a
10	chr19:39927495-39927545	PANC-1	pancreas:	n/a
11	chr19:39927495-39927545	AG09319	gingival:	n/a
12	chr19:39927495-39927545	SAEC	small airway:	n/a
13	chr19:39927495-39927545	NHDF-neo	bronchial:	n/a
14	chr19:39927495-39927545	PFSK-1	brain:	n/a
15	chr19:39927495-39927545	RPTEC	kidney:	n/a
16	chr19:39927495-39927545	K562	blood:	n/a
17	chr19:39927495-39927545	HCPEpiC	choroid plexus:	n/a
18	chr19:39927495-39927545	Jurkat	blood:	n/a
19	chr19:39927495-39927545	LNCaP	prostate:	n/a
20	chr19:39927495-39927545	GM19239	blood:	n/a
21	chr19:39927495-39927545	ProgFib	skin:	n/a
22	chr19:39927495-39927545	SK-N-SH	brain:	n/a
23	chr19:39927495-39927545	T-47D	breast:	n/a
24	chr19:39927495-39927545	NT2-D1	testis:	n/a
25	chr19:39927495-39927545	GM12892	blood:	n/a
26	chr19:39927495-39927545	HIPEpiC	eye:	n/a
27	chr19:39927495-39927545	HEEpiC	esophagus:	n/a
28	chr19:39927495-39927545	AoSMC	blood vessel:	n/a
29	chr19:39927495-39927545	SK-N-SH_RA	brain:	n/a
30	chr19:39927495-39927545	PrEC	prostate:	n/a
31	chr19:39927495-39927545	AG04449	skin:	fetal
32	chr19:39927495-39927545	BE2_C	brain:	n/a
33	chr19:39927495-39927545	AG10803	skin:	n/a
34	chr19:39927495-39927545	Caco-2	colon:	n/a
35	chr19:39927495-39927545	MCF-7	breast:	n/a
36	chr19:39927495-39927545	HPAEpiC	pulmonary alveolar:	n/a
37	chr19:39927495-39927545	HRE	kidney:	n/a
38	chr19:39927495-39927545	AG09309	skin:	n/a
39	chr19:39927495-39927545	BJ	skin:	n/a
40	chr19:39927495-39927545	IMR90	lung:	fetal
41	chr19:39927495-39927545	AG04450	lung:	fetal
42	chr19:39927495-39927545	HCF	heart:	n/a
43	chr19:39927495-39927545	Hela-S3	cervix:	n/a
44	chr19:39927495-39927545	GM12878	blood:	n/a
45	chr19:39927495-39927545	HepG2	liver:	n/a
46	chr19:39927495-39927545	NB4	blood:	n/a
47	chr19:39927495-39927545	Hepatocyte	liver:	n/a
48	chr19:39927495-39927545	H1-hESC	embryonic stem cell:	embryo
49	chr19:39927495-39927545	NH-A	brain:	n/a
50	chr19:39927495-39927545	HRPEpiC	eye:	n/a

(count:16 , 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	chr19:39619125..39620938-chr19:39926907..39929414,2	K562	blood:
4	chr19:39926041..39928299-chr19:40334872..40337810,2	MCF-7	breast:
5	chr19:39925979..39927964-chr19:39971323..39973932,2	K562	blood:
6	chr19:39926650..39928509-chr19:39969774..39972138,2	MCF-7	breast:
7	chr17:57919100..57920854-chr19:39926824..39928779,2	MCF-7	breast:
8	chr19:39925003..39927867-chr19:40028857..40032200,4	K562	blood:
9	chr19:39925068..39927999-chr19:40329043..40331985,2	K562	blood:
10	chr19:39925314..39927864-chr19:40336547..40338108,2	K562	blood:
11	chr19:39924469..39929022-chr19:39934307..39938518,21	MCF-7	breast:
12	chr19:39923771..39928393-chr19:40029138..40032183,4	MCF-7	breast:
13	chr19:39926032..39928483-chr19:40324303..40326455,2	MCF-7	breast:
14	chr19:39924549..39928313-chr19:39970394..39973544,4	MCF-7	breast:
15	chr19:39925083..39928891-chr19:40028576..40030872,3	K562	blood:
16	chr19:39923294..39928217-chr19:39969939..39976745,7	K562	blood:

No data

Variant related genes	Relation type
SUPT5H	TF binding region
ENSG00000213922	TF binding region
RPS16	TF binding region
ENSG00000213922	CpG island
SUPT5H	CpG island
RPS16	CpG island
ENSG00000130755	Chromatin interaction
ENSG00000105202	Chromatin interaction
ENSG00000105204	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000186838	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1130180	0.83[ASN][1000 genomes]
rs11881477	0.84[CEU][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12609112	0.81[ASN][1000 genomes]
rs12978920	0.85[ASN][1000 genomes]
rs12978954	0.81[ASN][1000 genomes]
rs12979605	0.82[ASN][1000 genomes]
rs12983040	0.80[ASN][1000 genomes]
rs1529732	0.83[ASN][1000 genomes]
rs1560730	0.91[CHB][hapmap];0.86[CHD][hapmap];0.80[ASN][1000 genomes]
rs17626	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17628	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1865091	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs1865092	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs1932	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[ASN][1000 genomes]
rs2009970	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs2060270	0.81[ASN][1000 genomes]
rs2060271	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs2116932	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs2288933	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs2288934	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs2304219	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs2353678	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2353679	0.88[ASN][1000 genomes]
rs251855	0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[ASN][1000 genomes]
rs251856	0.84[ASN][1000 genomes]
rs251857	0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[ASN][1000 genomes]
rs251858	0.83[ASN][1000 genomes]
rs251859	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs28528765	0.85[ASN][1000 genomes]
rs28649498	0.84[ASN][1000 genomes]
rs31726	0.80[CHD][hapmap]
rs31727	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs31728	0.86[CHB][hapmap]
rs4390710	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs4802026	0.85[ASN][1000 genomes]
rs4803237	0.83[ASN][1000 genomes]
rs4803240	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs4803241	0.80[ASN][1000 genomes]
rs4803245	0.86[CHB][hapmap]
rs4803246	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs4803247	0.82[CHB][hapmap]
rs480595	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs480656	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs481421	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs504017	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs564577	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs566130	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs59007555	0.81[ASN][1000 genomes]
rs640000	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6508862	0.86[ASN][1000 genomes]
rs651601	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs686956	0.83[ASN][1000 genomes]
rs7251652	0.81[ASN][1000 genomes]
rs7255253	0.83[ASN][1000 genomes]
rs73035416	0.83[ASN][1000 genomes]
rs73549933	0.83[ASN][1000 genomes]
rs8107194	0.91[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs8107647	0.83[ASN][1000 genomes]
rs8110134	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs8110716	0.87[ASN][1000 genomes]
rs878754	0.83[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs530411	BCAM	cis	parietal	SCAN
rs530411	RPS16	cis	lymphoblastoid	seeQTL
rs530411	NUMBL	cis	parietal	SCAN
rs530411	B3GNT8	cis	parietal	SCAN
rs530411	RPS16	cis	Lymphoblastoid	GTEx
rs530411	RPS16	Cis_1M	lymphoblastoid	RTeQTL
rs530411	RPS16	cis	Heart Left Ventricle	GTEx
rs530411	RPS16	cis	multi-tissue	Pritchard
rs530411	LOC441876///RPS16	Cis_1M	lymphoblastoid	RTeQTL
rs530411	RPS16	cis	Muscle Skeletal	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39925400-39927600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:39925400-39927600	Active TSS	GM12878-XiMat	blood
3	chr19:39925600-39927600	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr19:39925600-39927800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:39925800-39927600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr19:39925800-39927600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:39925800-39927600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr19:39925800-39927600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr19:39925800-39927800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:39925800-39927800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr19:39925800-39927800	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr19:39926400-39927800	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr19:39926600-39927600	Enhancers	Spleen	Spleen
14	chr19:39926600-39935200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:39926800-39927600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr19:39926800-39927600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:39926800-39927600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:39926800-39927600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr19:39926800-39927600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr19:39927000-39927600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:39927000-39927600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr19:39927000-39927600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:39927000-39927600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr19:39927000-39927600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:39927000-39927600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr19:39927000-39927600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:39927000-39927600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:39927000-39927600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:39927000-39927600	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr19:39927000-39927600	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr19:39927000-39927600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr19:39927000-39927600	Flanking Active TSS	Fetal Brain Female	brain
33	chr19:39927000-39927600	Flanking Active TSS	Fetal Heart	heart
34	chr19:39927000-39927600	Flanking Active TSS	Fetal Intestine Large	intestine
35	chr19:39927000-39927600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr19:39927000-39927600	Enhancers	Small Intestine	intestine
37	chr19:39927000-39927600	Flanking Active TSS	A549	lung
38	chr19:39927000-39927600	Flanking Active TSS	Dnd41	blood
39	chr19:39927000-39927600	Flanking Active TSS	NHEK	skin
40	chr19:39927000-39927600	Flanking Active TSS	Osteobl	bone
41	chr19:39927000-39927800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr19:39927000-39927800	Flanking Active TSS	Hela-S3	cervix
43	chr19:39927200-39927600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr19:39927200-39927600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:39927200-39927600	Enhancers	Primary B cells from cord blood	blood
46	chr19:39927200-39927600	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr19:39927200-39927600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr19:39927200-39927600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:39927200-39927600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:39927200-39927600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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