Variant report

Variant	rs3736329
Chromosome Location	chr19:41313202-41313203
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41282306..41285368-chr19:41311943..41315414,5	MCF-7	breast:
2	chr19:41253320..41258890-chr19:41311950..41315573,6	MCF-7	breast:
3	chr19:41221142..41224353-chr19:41311383..41314668,3	K562	blood:
4	chr19:41310513..41314653-chr19:41415794..41419669,4	K562	blood:
5	chr19:41312625..41314191-chr19:41317244..41319686,2	MCF-7	breast:
6	chr19:41223813..41226637-chr19:41310296..41313871,3	MCF-7	breast:
7	chr19:41267484..41269645-chr19:41312151..41314875,2	K562	blood:
8	chr19:41282692..41284743-chr19:41312820..41314498,2	MCF-7	breast:
9	chr19:41280805..41286068-chr19:41308324..41316733,13	K562	blood:
10	chr19:41261509..41264476-chr19:41312368..41314936,2	K562	blood:
11	chr19:41220938..41225137-chr19:41311275..41314518,5	K562	blood:
12	chr19:41220720..41224635-chr19:41312175..41316788,5	MCF-7	breast:
13	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:
14	chr19:41282175..41285758-chr19:41311471..41315456,8	K562	blood:
15	chr19:41221436..41223725-chr19:41310201..41314445,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000086544	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000198251	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000233622	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11547373	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12052092	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12151282	0.91[CEU][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs12973666	0.82[JPT][hapmap]
rs17726276	0.82[JPT][hapmap]
rs2279011	0.82[JPT][hapmap]
rs2305797	0.87[ASW][hapmap];0.84[CEU][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs35061187	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35405967	0.94[ASN][1000 genomes]
rs35858034	0.82[EUR][1000 genomes]
rs3733829	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776611	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41530251	0.84[ASW][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4802090	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4802091	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803369	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7245595	0.87[ASW][hapmap];0.92[CEU][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs73048928	0.93[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	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
2	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv521459	chr19:41313202-41333284	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3736329	KCNN4	cis	cerebellum	SCAN
rs3736329	DMPK	cis	cerebellum	SCAN
rs3736329	RPS19	cis	parietal	SCAN
rs3736329	CIC	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41305800-41316200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:41306400-41313600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:41306400-41313800	Genic enhancers	Fetal Thymus	thymus
4	chr19:41306400-41316200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr19:41306400-41316800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr19:41306600-41314000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:41306600-41314800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr19:41306800-41313400	Genic enhancers	Gastric	stomach
9	chr19:41307000-41313400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
10	chr19:41307000-41315800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:41308000-41313600	Weak transcription	Aorta	Aorta
12	chr19:41308200-41313400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr19:41308400-41313600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr19:41308400-41313600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:41308400-41316400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:41308600-41313600	Enhancers	Psoas Muscle	Psoas
17	chr19:41308800-41313400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:41308800-41313400	Genic enhancers	Fetal Intestine Large	intestine
19	chr19:41308800-41313600	Enhancers	Fetal Brain Male	brain
20	chr19:41308800-41313800	Genic enhancers	A549	lung
21	chr19:41308800-41314000	Genic enhancers	Esophagus	oesophagus
22	chr19:41309000-41313800	Genic enhancers	Fetal Muscle Leg	muscle
23	chr19:41309000-41316200	Genic enhancers	Placenta	Placenta
24	chr19:41309200-41313600	Enhancers	Right Atrium	heart
25	chr19:41309200-41314200	Genic enhancers	Fetal Stomach	stomach
26	chr19:41309200-41315600	Genic enhancers	Right Ventricle	heart
27	chr19:41309400-41316000	Genic enhancers	Spleen	Spleen
28	chr19:41309800-41313600	Genic enhancers	Fetal Intestine Small	intestine
29	chr19:41309800-41313600	Genic enhancers	Rectal Mucosa Donor 31	rectum
30	chr19:41309800-41313800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr19:41309800-41316200	Genic enhancers	Lung	lung
32	chr19:41309800-41316400	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr19:41310000-41315200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
34	chr19:41310400-41313600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
35	chr19:41310400-41314200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:41310600-41313600	Genic enhancers	GM12878-XiMat	blood
37	chr19:41311000-41314400	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr19:41311200-41313400	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr19:41311200-41314200	Genic enhancers	Primary B cells from cord blood	blood
40	chr19:41311200-41314600	Strong transcription	Hela-S3	cervix
41	chr19:41311200-41316400	Strong transcription	Dnd41	blood
42	chr19:41311400-41313400	Enhancers	Primary hematopoietic stem cells	blood
43	chr19:41311400-41313600	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr19:41311600-41313400	Enhancers	Placenta Amnion	Placenta Amnion
45	chr19:41311600-41313400	Genic enhancers	Rectal Mucosa Donor 29	rectum
46	chr19:41311800-41313400	Genic enhancers	HSMM	muscle
47	chr19:41311800-41313600	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr19:41311800-41313600	Enhancers	Colon Smooth Muscle	Colon
49	chr19:41312000-41313400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr19:41312000-41313400	Weak transcription	H9 Cell Line	embryonic stem cell

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