Variant report

Variant	rs2172350
Chromosome Location	chr8:19529575-19529576
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:19528114..19529694-chr8:19534657..19537045,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253270	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11204064	0.81[JPT][hapmap]
rs11776531	0.81[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11776539	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11778993	0.83[AMR][1000 genomes]
rs11785951	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11993323	0.91[JPT][hapmap]
rs1552778	0.83[YRI][hapmap]
rs1552779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17090675	0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs17128819	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17128822	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17481063	0.83[YRI][hapmap]
rs1994791	0.81[CEU][hapmap]
rs56355799	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59897738	0.87[ASN][1000 genomes]
rs61117033	0.82[ASN][1000 genomes]
rs62494489	0.83[ASN][1000 genomes]
rs6980879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7827153	0.86[ASW][hapmap];0.82[MKK][hapmap]
rs923768	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs958416	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv890627	chr8:19389865-19561997	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1021575	chr8:19430653-19623452	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1025271	chr8:19435147-19574969	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv6106	chr8:19499554-19544249	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1021731	chr8:19515149-19643313	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv890628	chr8:19527536-19540966	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2172350	PIWIL2	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19520400-19530400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr8:19520400-19539000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr8:19520400-19539400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr8:19520400-19539600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr8:19520600-19538800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr8:19520600-19538800	Weak transcription	Esophagus	oesophagus
7	chr8:19520600-19538800	Weak transcription	Gastric	stomach
8	chr8:19523200-19533200	Weak transcription	Pancreas	Pancrea
9	chr8:19523200-19534600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr8:19523400-19529600	Weak transcription	Fetal Brain Female	brain
11	chr8:19523600-19538600	Weak transcription	Brain Anterior Caudate	brain
12	chr8:19523800-19529600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr8:19523800-19540200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr8:19524200-19535200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr8:19524200-19539000	Weak transcription	Ovary	ovary
16	chr8:19525000-19533400	Weak transcription	Placenta	Placenta
17	chr8:19525200-19532800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr8:19525200-19533400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr8:19525400-19538800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr8:19525600-19530400	Weak transcription	Primary T cells from cord blood	blood
21	chr8:19525600-19530600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr8:19528400-19538400	Weak transcription	Fetal Heart	heart
23	chr8:19528600-19530600	Weak transcription	Hela-S3	cervix
24	chr8:19528600-19538600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr8:19528600-19540200	Weak transcription	Spleen	Spleen
26	chr8:19528800-19529600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr8:19528800-19530400	Weak transcription	Left Ventricle	heart
28	chr8:19528800-19530600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr8:19528800-19530800	Weak transcription	Brain Angular Gyrus	brain
30	chr8:19528800-19533000	Weak transcription	Right Atrium	heart
31	chr8:19528800-19536200	Weak transcription	Right Ventricle	heart
32	chr8:19528800-19538800	Weak transcription	Lung	lung
33	chr8:19529000-19530400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr8:19529000-19531000	Genic enhancers	A549	lung
35	chr8:19529200-19530600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr8:19529200-19532200	Strong transcription	Primary B cells from cord blood	blood
37	chr8:19529200-19533400	Weak transcription	Thymus	Thymus
38	chr8:19529400-19530000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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