Variant report

Variant	rs2909090
Chromosome Location	chr19:38188123-38188124
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
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	chr19:38188121-38188131	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:38188082-38188194	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:38187852-38188371	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:38188103-38188297	MCF-7	breast:	n/a	n/a
5	POLR2A	chr19:38188090-38188228	Gliobla	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:38188083-38188133	ProgFib	skin:	n/a
2	chr19:38188083-38188133	ECC-1	luminal epithelium:	n/a
3	chr19:38188083-38188133	AG10803	skin:	n/a
4	chr19:38188083-38188133	SK-N-SH	brain:	n/a
5	chr19:38188083-38188133	PrEC	prostate:	n/a
6	chr19:38188083-38188133	HCM	heart:	n/a
7	chr19:38188083-38188133	AG04449	skin:	fetal
8	chr19:38188083-38188133	HEEpiC	esophagus:	n/a
9	chr19:38188083-38188133	PFSK-1	brain:	n/a
10	chr19:38188083-38188133	GM06990	blood:	n/a
11	chr19:38188083-38188133	NHBE	bronchial:	n/a
12	chr19:38188083-38188133	H1-hESC	embryonic stem cell:	embryo
13	chr19:38188083-38188133	NT2-D1	testis:	n/a
14	chr19:38188083-38188133	A549	lung:	n/a
15	chr19:38188083-38188133	HNPCEpiC	eye:	n/a
16	chr19:38188083-38188133	AG04450	lung:	fetal
17	chr19:38188083-38188133	HepG2	liver:	n/a
18	chr19:38188083-38188133	AoSMC	blood vessel:	n/a
19	chr19:38188083-38188133	MCF10A-Er-Src	breast:	n/a
20	chr19:38188083-38188133	IMR90	lung:	fetal
21	chr19:38188083-38188133	LNCaP	prostate:	n/a
22	chr19:38188083-38188133	HCPEpiC	choroid plexus:	n/a
23	chr19:38188083-38188133	T-47D	breast:	n/a
24	chr19:38188083-38188133	U87	brain:	n/a
25	chr19:38188083-38188133	NHDF-neo	bronchial:	n/a
26	chr19:38188083-38188133	HL-60	blood:	n/a
27	chr19:38188083-38188133	NB4	blood:	n/a
28	chr19:38188083-38188133	HCT-116	colon:	n/a
29	chr19:38188083-38188133	HMEC	breast:	n/a
30	chr19:38188083-38188133	PANC-1	pancreas:	n/a
31	chr19:38188083-38188133	Hepatocyte	liver:	n/a
32	chr19:38188083-38188133	GM12891	blood:	n/a
33	chr19:38188083-38188133	HCF	heart:	n/a
34	chr19:38188083-38188133	HEK293	kidney:	embryo
35	chr19:38188083-38188133	HRE	kidney:	n/a
36	chr19:38188083-38188133	GM12892	blood:	n/a
37	chr19:38188083-38188133	CMK	blood:	n/a
38	chr19:38188083-38188133	HRCEpiC	kidney:	n/a
39	chr19:38188083-38188133	MCF-7	breast:	n/a
40	chr19:38188083-38188133	HUVEC	blood vessel:	n/a
41	chr19:38188083-38188133	Jurkat	blood:	n/a
42	chr19:38188083-38188133	K562	blood:	n/a
43	chr19:38188083-38188133	AG09309	skin:	n/a
44	chr19:38188083-38188133	Caco-2	colon:	n/a
45	chr19:38188083-38188133	HRPEpiC	eye:	n/a
46	chr19:38188083-38188133	SK-N-MC	brain:	n/a
47	chr19:38188083-38188133	HPAEpiC	pulmonary alveolar:	n/a
48	chr19:38188083-38188133	GM19239	blood:	n/a
49	chr19:38188083-38188133	SAEC	small airway:	n/a
50	chr19:38188083-38188133	HIPEpiC	eye:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38134173..38137861-chr19:38186479..38189500,3	K562	blood:

No data

Variant related genes	Relation type
ZFP30	TF binding region
ZNF781	TF binding region
ENSG00000267319	TF binding region
ZFP30	CpG island
ENSG00000267319	CpG island
ZNF781	CpG island

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs107696	0.80[YRI][hapmap]
rs171377	0.81[AFR][1000 genomes]
rs2216299	1.00[AMR][1000 genomes]
rs2248576	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2385006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs241934	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs241936	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs241938	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs241939	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs241945	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs241958	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs241961	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2891656	1.00[AMR][1000 genomes]
rs2909087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2909089	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2909091	1.00[AMR][1000 genomes]
rs2909094	1.00[AMR][1000 genomes]
rs2909095	1.00[AMR][1000 genomes]
rs2909096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2909099	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2909101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2909107	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972431	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972432	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972433	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972435	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972436	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972440	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972441	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972442	0.80[AFR][1000 genomes]
rs2972443	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972451	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972460	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3095723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3095725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3112436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34301943	1.00[AMR][1000 genomes]
rs3752364	1.00[CHB][hapmap]
rs59246699	1.00[AMR][1000 genomes]
rs61744939	1.00[AMR][1000 genomes]
rs6508734	1.00[AMR][1000 genomes]
rs6508740	1.00[AMR][1000 genomes]
rs7245613	1.00[AMR][1000 genomes]
rs7245750	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7249524	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7250160	1.00[AMR][1000 genomes]
rs7251623	1.00[AMR][1000 genomes]
rs7252424	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7259281	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8106132	1.00[AMR][1000 genomes]
rs8107942	1.00[AMR][1000 genomes]
rs8112992	0.83[LWK][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs856294	1.00[AMR][1000 genomes]
rs856296	1.00[AMR][1000 genomes]
rs856297	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs856303	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs978723	1.00[AMR][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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv978813	chr19:38187175-38188871	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38183200-38208800	Weak transcription	Fetal Heart	heart
2	chr19:38183400-38188800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr19:38183400-38190000	Weak transcription	Stomach Mucosa	stomach
4	chr19:38183600-38188800	Weak transcription	Fetal Kidney	kidney
5	chr19:38183600-38189400	Weak transcription	Psoas Muscle	Psoas
6	chr19:38183600-38190000	Weak transcription	Small Intestine	intestine
7	chr19:38184200-38188600	Weak transcription	Fetal Brain Male	brain
8	chr19:38184200-38201200	Weak transcription	Colonic Mucosa	Colon
9	chr19:38184400-38208800	Weak transcription	HepG2	liver
10	chr19:38186400-38191200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
11	chr19:38186800-38189200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr19:38186800-38189800	Strong transcription	Fetal Stomach	stomach
13	chr19:38186800-38191200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:38187000-38207800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:38187000-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:38187200-38190800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:38187200-38191600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr19:38187400-38188200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:38187400-38188200	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr19:38187400-38188200	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:38187400-38188200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
22	chr19:38187400-38188200	Strong transcription	Right Ventricle	heart
23	chr19:38187400-38188200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
24	chr19:38187400-38188200	ZNF genes & repeats	Spleen	Spleen
25	chr19:38187400-38188400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr19:38187400-38188400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr19:38187400-38188400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr19:38187400-38188400	ZNF genes & repeats	Aorta	Aorta
29	chr19:38187400-38188400	ZNF genes & repeats	Esophagus	oesophagus
30	chr19:38187400-38188400	Strong transcription	Fetal Intestine Small	intestine
31	chr19:38187400-38188400	ZNF genes & repeats	Gastric	stomach
32	chr19:38187400-38188400	ZNF genes & repeats	Lung	lung
33	chr19:38187400-38188400	ZNF genes & repeats	Ovary	ovary
34	chr19:38187400-38188400	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr19:38187400-38188600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
36	chr19:38187400-38188600	Strong transcription	Brain Substantia Nigra	brain
37	chr19:38187400-38189000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr19:38187400-38189200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
39	chr19:38187400-38189800	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr19:38187400-38190400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:38187400-38190600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:38187400-38190600	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr19:38187400-38190600	Strong transcription	Fetal Brain Female	brain
44	chr19:38187400-38190800	ZNF genes & repeats	Adipose Nuclei	Adipose
45	chr19:38187400-38190800	Strong transcription	Brain Angular Gyrus	brain
46	chr19:38187400-38190800	Strong transcription	Brain Germinal Matrix	brain
47	chr19:38187400-38190800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:38187400-38190800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
49	chr19:38187400-38190800	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr19:38187400-38190800	ZNF genes & repeats	HSMM	muscle

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