Variant report

Variant	rs855603
Chromosome Location	chr19:38560691-38560692
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38549096..38551828-chr19:38559673..38561442,2	MCF-7	breast:
2	chr19:38395351..38397718-chr19:38560093..38561831,2	MCF-7	breast:
3	chr19:38550744..38552362-chr19:38559660..38561600,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10405667	0.87[EUR][1000 genomes]
rs10412762	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs10413751	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10414433	0.82[CEU][hapmap]
rs10420506	0.81[JPT][hapmap]
rs10422665	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1568975	0.87[EUR][1000 genomes]
rs1614979	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs1622409	0.88[EUR][1000 genomes]
rs1625884	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1654347	0.85[ASN][1000 genomes]
rs1654349	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs1654350	0.85[ASN][1000 genomes]
rs1654352	0.85[ASN][1000 genomes]
rs1654355	0.87[EUR][1000 genomes]
rs1654357	0.88[EUR][1000 genomes]
rs1654358	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1654359	0.88[EUR][1000 genomes]
rs1654365	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1654367	0.89[EUR][1000 genomes]
rs1725461	0.86[EUR][1000 genomes]
rs1725470	0.85[ASN][1000 genomes]
rs1725473	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1725475	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs1725476	0.85[ASN][1000 genomes]
rs1725479	0.88[EUR][1000 genomes]
rs1725506	0.83[AFR][1000 genomes]
rs1725507	0.80[AFR][1000 genomes]
rs1725508	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1725509	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1725510	0.85[ASN][1000 genomes]
rs1725512	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs28412601	0.90[ASN][1000 genomes]
rs28587798	0.96[AFR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3760882	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3810356	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4802233	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs4802239	0.86[EUR][1000 genomes]
rs4802256	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs4803786	0.81[EUR][1000 genomes]
rs4803828	0.81[JPT][hapmap]
rs4803829	0.81[JPT][hapmap]
rs56166457	0.85[EUR][1000 genomes]
rs57585457	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs57999412	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs58152231	0.88[EUR][1000 genomes]
rs59185302	0.81[EUR][1000 genomes]
rs59579475	0.85[EUR][1000 genomes]
rs59924887	0.81[EUR][1000 genomes]
rs61388128	0.81[EUR][1000 genomes]
rs705505	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7257303	0.85[ASN][1000 genomes]
rs729625	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs729626	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs735615	0.88[EUR][1000 genomes]
rs8105468	0.81[EUR][1000 genomes]
rs855597	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855598	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs855599	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs855600	0.96[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855601	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855602	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855619	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs855621	0.88[EUR][1000 genomes]
rs855623	0.88[EUR][1000 genomes]
rs855624	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs855630	0.81[EUR][1000 genomes]
rs855633	0.94[CEU][hapmap]
rs855636	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[ASN][1000 genomes]
rs855637	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs855638	0.88[EUR][1000 genomes]
rs855640	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs855641	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs860623	0.94[CEU][hapmap]
rs863020	0.94[CEU][hapmap]
rs941039	0.94[CEU][hapmap]
rs941040	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs9941467	0.87[CEU][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs855603	DPF1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
2	chr19:38539000-38572000	Weak transcription	Right Ventricle	heart
3	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
4	chr19:38543800-38563200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr19:38546600-38572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr19:38547000-38563600	Weak transcription	Fetal Lung	lung
7	chr19:38547200-38561400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:38549200-38564800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr19:38549200-38572000	Weak transcription	Liver	Liver
10	chr19:38549600-38572600	Weak transcription	Thymus	Thymus
11	chr19:38550000-38561000	Weak transcription	Hela-S3	cervix
12	chr19:38550000-38570400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr19:38550800-38563400	Weak transcription	Spleen	Spleen
14	chr19:38550800-38565200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr19:38550800-38570000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr19:38550800-38572200	Weak transcription	Colonic Mucosa	Colon
17	chr19:38550800-38590000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr19:38551000-38572000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr19:38551200-38562200	Weak transcription	Primary T cells from cord blood	blood
20	chr19:38551200-38562600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr19:38551200-38563600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr19:38551200-38567000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr19:38551400-38562400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:38551400-38567000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:38552400-38560800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:38552400-38561000	Weak transcription	NHEK	skin
28	chr19:38552400-38561200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:38553200-38570400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:38553800-38561200	Weak transcription	NH-A	brain
31	chr19:38553800-38561400	Weak transcription	Esophagus	oesophagus
32	chr19:38553800-38561400	Weak transcription	Lung	lung
33	chr19:38553800-38572000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:38554200-38561400	Weak transcription	Pancreas	Pancrea
35	chr19:38554200-38572600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr19:38554400-38561000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:38554400-38564600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:38554600-38561000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:38554600-38567000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr19:38554600-38570400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:38554600-38571800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr19:38554800-38561400	Weak transcription	HSMM	muscle
43	chr19:38554800-38562000	Strong transcription	Fetal Intestine Small	intestine
44	chr19:38554800-38563600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr19:38554800-38571800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr19:38554800-38573200	Weak transcription	Brain Angular Gyrus	brain
47	chr19:38554800-38580200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr19:38555000-38562000	Weak transcription	Fetal Stomach	stomach
49	chr19:38555000-38563400	Weak transcription	Fetal Muscle Leg	muscle
50	chr19:38555000-38570800	Weak transcription	Fetal Intestine Large	intestine

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