Variant report

Variant	rs10415219
Chromosome Location	chr19:39150235-39150236
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39150052..39153067-chr19:39197622..39201361,3	MCF-7	breast:
2	chr19:39148794..39150832-chr3:147109413..147111570,2	MCF-7	breast:
3	chr19:39148867..39151861-chr19:39164065..39166508,2	K562	blood:
4	chr19:39150082..39153309-chr19:39178166..39180062,3	MCF-7	breast:
5	chr19:39149024..39154711-chr19:39158901..39163144,7	MCF-7	breast:
6	chr19:39147918..39151863-chr19:39340642..39342980,4	MCF-7	breast:
7	chr19:39147345..39151436-chr19:39186794..39189528,4	MCF-7	breast:
8	chr19:39146061..39150470-chr19:39339841..39342984,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000152977	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000174963	Chromatin interaction
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10403540	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10404257	0.93[ASN][1000 genomes]
rs10406778	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10415646	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10421560	1.00[CEU][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10426809	0.83[CHD][hapmap];0.80[JPT][hapmap]
rs11083475	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12460849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12462270	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13343794	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13344413	0.92[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs16972767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279144	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2303040	1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28488032	0.84[ASN][1000 genomes]
rs28624276	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3745859	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3786835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3786839	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs3786845	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3786848	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3786851	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3810341	0.98[ASN][1000 genomes]
rs55876653	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56113315	0.83[EUR][1000 genomes]
rs56365761	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121814	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62121816	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62121818	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7251903	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs7252589	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7254100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8107416	0.92[CEU][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap]
rs8111746	0.83[ASN][1000 genomes]
rs883394	0.81[EUR][1000 genomes]
rs883433	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs979971	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs979972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	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
2	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
3	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
4	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
5	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10415219	ZNF526	cis	cerebellum	SCAN
rs10415219	LGALS17A	cis	cerebellum	SCAN
rs10415219	PSG3	cis	parietal	SCAN
rs10415219	TMEM145	cis	parietal	SCAN
rs10415219	ERCC1	cis	cerebellum	SCAN
rs10415219	MEGF8	cis	parietal	SCAN
rs10415219	RPS16	cis	parietal	SCAN

Chromatin state (count:124 , 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	chr19:39140600-39151000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
4	chr19:39142200-39151800	Enhancers	Brain Cingulate Gyrus	brain
5	chr19:39142600-39150400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:39142800-39151200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr19:39143400-39150600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:39143400-39154400	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr19:39143800-39153200	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr19:39144200-39150400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr19:39144200-39153400	Genic enhancers	K562	blood
12	chr19:39144400-39150600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr19:39144400-39152200	Enhancers	Right Ventricle	heart
14	chr19:39144600-39154000	Enhancers	Right Atrium	heart
15	chr19:39144800-39154000	Genic enhancers	Fetal Intestine Large	intestine
16	chr19:39145200-39153400	Genic enhancers	Fetal Intestine Small	intestine
17	chr19:39145600-39150600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr19:39146800-39151800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:39147000-39150400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr19:39147000-39151400	Enhancers	Brain Anterior Caudate	brain
21	chr19:39147400-39151400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr19:39147400-39160000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr19:39147600-39151400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:39147600-39151600	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr19:39147600-39154000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr19:39147600-39154000	Enhancers	Brain Angular Gyrus	brain
27	chr19:39147800-39151000	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr19:39147800-39151200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:39147800-39160800	Enhancers	Placenta	Placenta
30	chr19:39148000-39150400	Bivalent Enhancer	Fetal Thymus	thymus
31	chr19:39148000-39151000	Enhancers	Fetal Kidney	kidney
32	chr19:39148000-39152800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr19:39148200-39150600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:39148200-39151400	Enhancers	Small Intestine	intestine
35	chr19:39148400-39150600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:39148600-39150600	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr19:39148600-39151800	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr19:39148600-39153400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
39	chr19:39148800-39150400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr19:39148800-39150400	Flanking Active TSS	Hela-S3	cervix
41	chr19:39148800-39151200	Enhancers	Fetal Stomach	stomach
42	chr19:39148800-39151200	Weak transcription	Lung	lung
43	chr19:39148800-39151400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:39148800-39153000	Weak transcription	Primary B cells from cord blood	blood
45	chr19:39149000-39150400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:39149000-39150400	Flanking Active TSS	Osteobl	bone
47	chr19:39149000-39150600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:39149000-39150800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr19:39149000-39151400	Enhancers	Primary T cells fromperipheralblood	blood
50	chr19:39149000-39151400	Enhancers	Duodenum Mucosa	Duodenum

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