Variant report

Variant	rs10415548
Chromosome Location	chr19:38425053-38425054
allele	C/T
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	chr19:38395556..38401665-chr19:38419693..38425913,12	MCF-7	breast:
2	chr19:38393450..38400778-chr19:38419865..38427350,17	MCF-7	breast:
3	chr19:38424099..38425742-chr19:38427157..38428812,2	K562	blood:
4	chr19:38405526..38407086-chr19:38423053..38425586,2	MCF-7	breast:
5	chr19:38423561..38425591-chr19:38488215..38490133,2	MCF-7	breast:
6	chr19:38424879..38427033-chr19:38465266..38467452,2	MCF-7	breast:
7	chr19:38423922..38426366-chr19:38436893..38438716,2	MCF-7	breast:
8	chr19:38423743..38426556-chr19:38482738..38484356,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10404159	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10404567	0.88[CEU][hapmap]
rs10415399	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10420746	0.83[CEU][hapmap]
rs11083441	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1119229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs12608883	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1291	0.88[CEU][hapmap]
rs12973580	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12974225	0.88[CEU][hapmap]
rs1643460	0.83[EUR][1000 genomes]
rs1643461	0.87[EUR][1000 genomes]
rs1643466	0.82[CEU][hapmap]
rs1643467	0.83[CEU][hapmap]
rs1643468	0.83[CEU][hapmap]
rs1725481	0.83[CEU][hapmap]
rs1725482	0.88[CEU][hapmap]
rs1725499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075281	0.83[CEU][hapmap]
rs241932	0.88[CEU][hapmap]
rs28460297	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353410	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs353411	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs353414	0.83[CEU][hapmap]
rs353415	0.83[CEU][hapmap]
rs353423	0.83[CEU][hapmap]
rs3786869	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3865514	1.00[YRI][hapmap]
rs4239516	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802144	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4802147	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802151	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4803524	0.88[CEU][hapmap]
rs4803551	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs705492	0.83[CEU][hapmap]
rs705493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs705494	0.88[CEU][hapmap]
rs705495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705499	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7250409	0.88[CEU][hapmap]
rs8102579	0.88[CEU][hapmap]
rs8108434	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109053	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109835	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8110284	0.83[CEU][hapmap]
rs8112706	0.83[CEU][hapmap]
rs8113273	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8113521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs833895	0.83[CEU][hapmap]
rs833926	0.83[CEU][hapmap]
rs856300	0.82[CEU][hapmap]
rs856304	0.88[CEU][hapmap]

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	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	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1820125	chr19:38424904-38427984	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr19:38411800-38426200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr19:38418800-38425600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:38421800-38425400	Enhancers	Fetal Muscle Trunk	muscle
6	chr19:38421800-38425400	Enhancers	Fetal Muscle Leg	muscle
7	chr19:38422000-38426400	Weak transcription	Primary T cells from cord blood	blood
8	chr19:38422200-38425600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:38423000-38425200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:38423000-38425400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:38423000-38438200	Weak transcription	Brain Angular Gyrus	brain
12	chr19:38423200-38425800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr19:38423200-38426000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:38423200-38426200	Weak transcription	Ovary	ovary
15	chr19:38423200-38426600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr19:38423200-38443000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr19:38423400-38425200	Enhancers	HSMM	muscle
18	chr19:38423400-38425200	Enhancers	NH-A	brain
19	chr19:38423400-38425800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr19:38423400-38426000	Weak transcription	Brain Hippocampus Middle	brain
21	chr19:38423400-38426000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:38423400-38426400	Weak transcription	Brain Germinal Matrix	brain
23	chr19:38423400-38427600	Enhancers	Liver	Liver
24	chr19:38423400-38433800	Weak transcription	Thymus	Thymus
25	chr19:38423600-38425200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr19:38423600-38425200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr19:38423600-38425200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:38423600-38425400	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr19:38423600-38425600	Weak transcription	Brain Anterior Caudate	brain
30	chr19:38423600-38425800	Enhancers	HMEC	breast
31	chr19:38423600-38444400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:38424000-38425400	Genic enhancers	Primary B cells from cord blood	blood
33	chr19:38424000-38425400	Enhancers	Fetal Stomach	stomach
34	chr19:38424000-38426000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr19:38424200-38425200	Enhancers	Colon Smooth Muscle	Colon
36	chr19:38424200-38425200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr19:38424200-38425800	Enhancers	Pancreas	Pancrea
38	chr19:38424400-38425400	Transcr. at gene 5' and 3'	A549	lung
39	chr19:38424400-38426000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:38424400-38426400	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr19:38424400-38426800	Weak transcription	Fetal Brain Female	brain
42	chr19:38424400-38427000	Enhancers	Gastric	stomach
43	chr19:38424400-38428000	Genic enhancers	Primary B cells from peripheral blood	blood
44	chr19:38424600-38425200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:38424600-38425200	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr19:38424600-38425200	Enhancers	Osteobl	bone
47	chr19:38424600-38425400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr19:38424600-38425400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr19:38424600-38425600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:38424600-38425800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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