Variant report

Variant	rs2305797
Chromosome Location	chr19:41269076-41269077
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41268169-41273504	K562	blood:	n/a	n/a
2	POLR2A	chr19:41268239-41270275	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:41268597-41270263	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:41269036-41269398	GM12891	blood:	n/a	n/a
5	POLR2A	chr19:41269000-41270549	A549	lung:	n/a	n/a
6	POLR2A	chr19:41268317-41270228	K562	blood:	n/a	n/a
7	POLR2A	chr19:41268962-41269665	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:41268992-41269462	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:41268874-41269485	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:41268980-41270353	GM12891	blood:	n/a	n/a
11	POLR2A	chr19:41268988-41269498	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr19:41268967-41270158	K562	blood:	n/a	n/a
13	POLR2A	chr19:41268949-41269082	K562	blood:	n/a	n/a
14	POLR2A	chr19:41268608-41270314	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr19:41268820-41270708	HepG2	liver:	n/a	n/a
16	POLR2A	chr19:41268458-41269385	HepG2	liver:	n/a	n/a
17	POLR2A	chr19:41269070-41269269	A549	lung:	n/a	n/a
18	POLR2A	chr19:41268987-41269399	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr19:41268920-41269766	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr19:41268673-41270330	GM12892	blood:	n/a	n/a
21	POLR2A	chr19:41269037-41269297	A549	lung:	n/a	n/a
22	POLR2A	chr19:41268985-41269586	GM12892	blood:	n/a	n/a
23	POLR2A	chr19:41268710-41270206	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr19:41268982-41269355	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:41268399-41270345	HL-60	blood:	n/a	n/a
26	POLR2A	chr19:41268908-41270245	K562	blood:	n/a	n/a
27	POLR2A	chr19:41268840-41270318	SK-N-MC	brain:	n/a	n/a
28	POLR2A	chr19:41268876-41269178	K562	blood:	n/a	n/a
29	POLR2A	chr19:41269028-41269416	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41266506..41270324-chr19:41304182..41308237,4	MCF-7	breast:
2	chr19:41267484..41269645-chr19:41312151..41314875,2	K562	blood:
3	chr19:41260139..41263549-chr19:41263654..41270764,10	MCF-7	breast:
4	chr19:41268609..41270148-chr19:41279766..41281327,2	K562	blood:
5	chr19:41267917..41272263-chr19:41274538..41279747,5	K562	blood:
6	chr19:41220988..41222886-chr19:41267608..41270115,2	MCF-7	breast:
7	chr19:41224657..41226437-chr19:41266206..41269077,2	MCF-7	breast:

No data

Variant related genes	Relation type
SNRPA	TF binding region
ENSG00000077312	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000268797	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11547373	0.84[EUR][1000 genomes]
rs12151282	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12973666	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17726276	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2279011	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2561547	1.00[LWK][hapmap]
rs35858034	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3733829	0.87[ASW][hapmap];0.84[CEU][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs3736329	0.87[ASW][hapmap];0.84[CEU][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs3776611	0.81[EUR][1000 genomes]
rs41530251	0.85[MKK][hapmap]
rs4802090	0.81[EUR][1000 genomes]
rs4802091	0.80[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs4803369	0.87[ASW][hapmap];0.84[CEU][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs7245595	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7254192	0.98[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	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1802033	chr19:41256131-41284240	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	40 gene(s)	inside rSNPs	diseases
4	esv1801805	chr19:41256581-41284363	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	37 gene(s)	inside rSNPs	diseases
5	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2305797	KCNN4	cis	cerebellum	SCAN
rs2305797	RPS19	cis	parietal	SCAN
rs2305797	CNFN	cis	cerebellum	SCAN
rs2305797	TULP2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41258000-41283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41259000-41275200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:41259200-41272800	Strong transcription	H1 Cell Line	embryonic stem cell
4	chr19:41260200-41272000	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr19:41260400-41271800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:41260600-41272400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:41260600-41272600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:41260600-41277200	Strong transcription	Fetal Brain Female	brain
9	chr19:41260800-41272200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr19:41260800-41272200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr19:41260800-41272400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr19:41260800-41272400	Strong transcription	Brain Anterior Caudate	brain
13	chr19:41260800-41283200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr19:41261000-41271800	Strong transcription	HSMM	muscle
15	chr19:41261000-41272200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:41261000-41272200	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr19:41261200-41272200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:41261200-41272200	Strong transcription	Fetal Lung	lung
19	chr19:41261200-41273000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr19:41261200-41273600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr19:41261600-41272000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:41261600-41272000	Strong transcription	Osteobl	bone
23	chr19:41261600-41272200	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr19:41261600-41272200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:41261600-41275000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:41261600-41275200	Strong transcription	Fetal Muscle Trunk	muscle
27	chr19:41261800-41272000	Strong transcription	Ovary	ovary
28	chr19:41261800-41272200	Strong transcription	Primary hematopoietic stem cells	blood
29	chr19:41261800-41272200	Strong transcription	NHLF	lung
30	chr19:41261800-41272400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:41261800-41272400	Strong transcription	Fetal Intestine Large	intestine
32	chr19:41261800-41272400	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr19:41261800-41272600	Strong transcription	Right Ventricle	heart
34	chr19:41261800-41276800	Strong transcription	Fetal Intestine Small	intestine
35	chr19:41261800-41278200	Strong transcription	Fetal Stomach	stomach
36	chr19:41261800-41282800	Weak transcription	Right Atrium	heart
37	chr19:41262000-41270000	Weak transcription	Fetal Heart	heart
38	chr19:41262000-41272200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:41262000-41272200	Strong transcription	K562	blood
40	chr19:41262000-41273400	Strong transcription	Brain Germinal Matrix	brain
41	chr19:41262000-41276200	Strong transcription	Thymus	Thymus
42	chr19:41262200-41273800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr19:41262400-41270400	Strong transcription	Fetal Thymus	thymus
44	chr19:41262400-41272400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:41262400-41273000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr19:41262600-41271800	Strong transcription	Fetal Kidney	kidney
47	chr19:41262600-41272000	Strong transcription	Brain Angular Gyrus	brain
48	chr19:41262600-41272200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr19:41262600-41272200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:41262600-41272200	Strong transcription	Left Ventricle	heart

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