Variant report

Variant	rs1725475
Chromosome Location	chr19:38552079-38552080
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38395738..38398220-chr19:38547451..38552123,4	MCF-7	breast:
2	chr19:38543891..38548790-chr19:38549215..38554298,5	MCF-7	breast:
3	chr19:38550744..38552362-chr19:38559660..38561600,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000221258	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10412762	0.81[JPT][hapmap]
rs10413751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10414433	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10420506	0.81[JPT][hapmap]
rs10422665	0.81[JPT][hapmap]
rs1612361	0.92[EUR][1000 genomes]
rs1614979	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1654341	0.92[EUR][1000 genomes]
rs1654343	0.93[EUR][1000 genomes]
rs1654347	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654349	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654350	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654352	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654365	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs1725458	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1725462	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1725470	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725476	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725504	0.82[CEU][hapmap];0.95[TSI][hapmap]
rs1725506	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1725507	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1725508	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725509	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725510	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725512	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs28587798	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4802233	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4802256	0.81[JPT][hapmap]
rs4803828	0.81[JPT][hapmap]
rs4803829	0.81[JPT][hapmap]
rs57585457	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57999412	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257303	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729626	0.82[ASN][1000 genomes]
rs855597	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs855598	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855599	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855600	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs855601	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs855602	0.85[ASN][1000 genomes]
rs855603	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs855619	0.82[ASN][1000 genomes]
rs855624	0.82[ASN][1000 genomes]
rs855636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941040	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs9941467	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1060359	chr19:38512719-38552438	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1062518	chr19:38540454-38564913	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1725475	ZNF404	cis	cerebellum	SCAN
rs1725475	CCDC8	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38522000-38553600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
3	chr19:38538400-38552800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:38539000-38572000	Weak transcription	Right Ventricle	heart
5	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
6	chr19:38543400-38553600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:38543800-38563200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr19:38545800-38553600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr19:38546400-38553600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr19:38546600-38553600	Weak transcription	Brain Substantia Nigra	brain
11	chr19:38546600-38554000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:38546600-38572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr19:38547000-38553400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr19:38547000-38553600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:38547000-38554800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr19:38547000-38563600	Weak transcription	Fetal Lung	lung
17	chr19:38547200-38561400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:38547600-38553200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:38548600-38554400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr19:38548600-38555000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr19:38549000-38553000	Weak transcription	Brain Angular Gyrus	brain
22	chr19:38549000-38553000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr19:38549000-38553200	Weak transcription	Fetal Stomach	stomach
24	chr19:38549000-38553600	Weak transcription	Brain Hippocampus Middle	brain
25	chr19:38549200-38552600	Weak transcription	Lung	lung
26	chr19:38549200-38552800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:38549200-38553000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr19:38549200-38553400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:38549200-38564800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr19:38549200-38572000	Weak transcription	Liver	Liver
31	chr19:38549400-38552200	Weak transcription	Fetal Intestine Large	intestine
32	chr19:38549400-38552200	Weak transcription	Pancreas	Pancrea
33	chr19:38549400-38552600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr19:38549400-38553000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:38549400-38553000	Weak transcription	Gastric	stomach
36	chr19:38549400-38553600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr19:38549400-38560000	Weak transcription	Psoas Muscle	Psoas
38	chr19:38549600-38553600	Weak transcription	Esophagus	oesophagus
39	chr19:38549600-38572600	Weak transcription	Thymus	Thymus
40	chr19:38550000-38552200	Enhancers	A549	lung
41	chr19:38550000-38561000	Weak transcription	Hela-S3	cervix
42	chr19:38550000-38570400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr19:38550200-38552200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:38550200-38552600	Enhancers	HUVEC	blood vessel
45	chr19:38550200-38553000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr19:38550800-38552600	Enhancers	Osteobl	bone
47	chr19:38550800-38553200	Enhancers	NHLF	lung
48	chr19:38550800-38563400	Weak transcription	Spleen	Spleen
49	chr19:38550800-38565200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr19:38550800-38570000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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