Variant report

Variant	rs13344413
Chromosome Location	chr19:39143289-39143290
allele	A/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39141347..39144030-chr19:39208371..39211834,3	MCF-7	breast:
2	chr19:39108181..39110451-chr19:39143165..39144685,2	MCF-7	breast:
3	chr19:39142774..39144585-chr19:39172676..39174844,2	MCF-7	breast:
4	chr19:39143284..39145449-chr19:39147356..39150112,2	K562	blood:
5	chr19:39142246..39144499-chr19:39217661..39220429,2	K562	blood:
6	chr19:39141727..39145361-chr19:39153035..39156463,3	K562	blood:
7	chr19:39137047..39143767-chr19:39341076..39344906,12	MCF-7	breast:
8	chr19:39141654..39143815-chr19:39327217..39328958,2	MCF-7	breast:
9	chr19:39136970..39140096-chr19:39140173..39145438,10	MCF-7	breast:
10	chr19:39140411..39144509-chr19:39172304..39176724,4	K562	blood:
11	chr19:39137026..39140722-chr19:39142479..39146305,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000178982	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10405232	1.00[YRI][hapmap]
rs10405261	1.00[YRI][hapmap]
rs10413936	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs10415219	0.92[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs10420476	1.00[YRI][hapmap]
rs10421087	1.00[YRI][hapmap]
rs10421560	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs11083475	0.92[CEU][hapmap]
rs12460849	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs12462270	0.96[CEU][hapmap]
rs16972767	0.96[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2279144	0.88[CEU][hapmap];0.93[TSI][hapmap]
rs2287734	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2303040	0.86[ASW][hapmap];0.92[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2368477	1.00[LWK][hapmap]
rs3745859	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs3786835	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs3786837	0.86[EUR][1000 genomes]
rs3786839	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs3786845	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs3786851	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs4802887	1.00[ASW][hapmap]
rs55876653	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs56365761	0.91[EUR][1000 genomes]
rs62121814	0.90[EUR][1000 genomes]
rs7251903	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs7254100	0.91[CEU][hapmap]
rs8107416	0.88[CEU][hapmap];0.91[TSI][hapmap]
rs883433	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs979971	0.92[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs979972	0.92[CEU][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
7	nsv911667	chr19:39119898-39143289	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13344413	PRR19	cis	parietal	SCAN
rs13344413	RPS16	cis	parietal	SCAN
rs13344413	TMEM145	cis	parietal	SCAN
rs13344413	PSG3	cis	parietal	SCAN
rs13344413	MEGF8	cis	parietal	SCAN
rs13344413	ERCC1	cis	cerebellum	SCAN
rs13344413	ZNF526	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39138600-39152200	Transcr. at gene 5' and 3'	A549	lung
2	chr19:39138800-39143800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr19:39139600-39143400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
4	chr19:39139800-39143600	Flanking Active TSS	Duodenum Mucosa	Duodenum
5	chr19:39140000-39143400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr19:39140400-39146800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:39140600-39143400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:39140600-39151000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr19:39140800-39143400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr19:39140800-39145200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr19:39141000-39144000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:39141200-39143400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr19:39141200-39143600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr19:39141200-39143600	Enhancers	Ovary	ovary
15	chr19:39141200-39143600	Enhancers	Spleen	Spleen
16	chr19:39141200-39143600	Flanking Active TSS	HepG2	liver
17	chr19:39141200-39143800	Enhancers	Placenta	Placenta
18	chr19:39141200-39144400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:39141200-39144400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr19:39141200-39145600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr19:39141200-39147000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr19:39141200-39147600	Enhancers	Primary hematopoietic stem cells	blood
23	chr19:39141200-39148600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:39141200-39148800	Enhancers	Placenta Amnion	Placenta Amnion
25	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
26	chr19:39141400-39143400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:39141400-39143400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:39141400-39143600	Enhancers	Lung	lung
29	chr19:39141400-39143600	Enhancers	Pancreas	Pancrea
30	chr19:39141400-39143800	Enhancers	Fetal Muscle Trunk	muscle
31	chr19:39141400-39144400	Enhancers	Primary B cells from cord blood	blood
32	chr19:39141400-39145400	Enhancers	Fetal Kidney	kidney
33	chr19:39141400-39146000	Enhancers	Brain Anterior Caudate	brain
34	chr19:39141400-39146400	Enhancers	H1 Cell Line	embryonic stem cell
35	chr19:39141400-39147000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr19:39141400-39147800	Enhancers	Small Intestine	intestine
37	chr19:39141400-39148000	Genic enhancers	Fetal Muscle Leg	muscle
38	chr19:39141600-39144200	Flanking Active TSS	NHEK	skin
39	chr19:39141600-39145200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr19:39141800-39143600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr19:39141800-39144400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:39141800-39144600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr19:39141800-39146800	Enhancers	Fetal Lung	lung
44	chr19:39141800-39147200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:39142000-39143400	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr19:39142000-39143600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:39142000-39143800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:39142000-39144000	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr19:39142000-39144000	Enhancers	Left Ventricle	heart
50	chr19:39142000-39144200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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