Variant report

Variant	rs353411
Chromosome Location	chr19:38442897-38442898
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38440998..38442982-chr19:38537686..38540589,2	MCF-7	breast:
2	chr19:38432664..38434680-chr19:38442017..38444946,2	MCF-7	breast:
3	chr19:38395717..38398405-chr19:38438245..38443084,4	MCF-7	breast:
4	chr19:38441551..38443321-chr19:38443505..38445243,2	K562	blood:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10404159	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10404567	0.88[CEU][hapmap]
rs10415399	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10415548	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]
rs10420746	0.83[CEU][hapmap]
rs11083441	0.91[EUR][1000 genomes]
rs1119229	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs12608883	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12973580	0.90[EUR][1000 genomes]
rs1643460	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1643461	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][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];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2075281	0.83[CEU][hapmap]
rs241932	0.88[CEU][hapmap]
rs28460297	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs353410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353414	0.83[CEU][hapmap]
rs353415	0.83[CEU][hapmap]
rs353423	0.83[CEU][hapmap]
rs3786869	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4239516	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4802144	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4802147	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4802151	0.83[EUR][1000 genomes]
rs4803524	0.88[CEU][hapmap]
rs4803551	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4803573	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs705491	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs705492	0.83[CEU][hapmap]
rs705493	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs705494	0.88[CEU][hapmap]
rs705495	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs705499	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250409	0.88[CEU][hapmap]
rs8102579	0.88[CEU][hapmap]
rs8108434	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8109053	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8109835	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8110284	0.83[CEU][hapmap]
rs8112706	0.83[CEU][hapmap]
rs8113273	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8113521	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[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: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	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
3	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

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38423200-38443000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:38423600-38444400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:38424800-38444000	Weak transcription	NHDF-Ad	bronchial
4	chr19:38425000-38454000	Weak transcription	HSMMtube	muscle
5	chr19:38426400-38444000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr19:38426600-38448200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr19:38426600-38450800	Weak transcription	Ovary	ovary
8	chr19:38426800-38443800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr19:38427000-38444000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:38427000-38444000	Weak transcription	Fetal Brain Female	brain
11	chr19:38427200-38443800	Weak transcription	NHEK	skin
12	chr19:38427200-38444200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:38427400-38443600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:38427600-38443600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:38428600-38443400	Weak transcription	Fetal Stomach	stomach
16	chr19:38429200-38443800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr19:38430600-38444000	Weak transcription	HSMM	muscle
18	chr19:38430600-38453600	Weak transcription	Aorta	Aorta
19	chr19:38432400-38443200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr19:38432600-38443400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:38432800-38443800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:38433000-38444000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:38434000-38447800	Weak transcription	Hela-S3	cervix
24	chr19:38434200-38443000	Weak transcription	Right Atrium	heart
25	chr19:38434400-38444200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:38434400-38451800	Weak transcription	Primary T cells from cord blood	blood
27	chr19:38435200-38444000	Weak transcription	Colonic Mucosa	Colon
28	chr19:38436600-38443800	Weak transcription	Fetal Intestine Large	intestine
29	chr19:38436600-38444000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr19:38438400-38455600	Enhancers	Primary B cells from peripheral blood	blood
31	chr19:38438800-38443400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:38439000-38445200	Weak transcription	Fetal Heart	heart
33	chr19:38439600-38443800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr19:38439600-38453000	Weak transcription	Gastric	stomach
35	chr19:38439800-38443400	Weak transcription	Pancreas	Pancrea
36	chr19:38440000-38444200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr19:38440000-38446400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr19:38440800-38449600	Enhancers	Primary B cells from cord blood	blood
39	chr19:38441000-38445200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr19:38441000-38446600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr19:38441200-38443000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:38441400-38443400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr19:38441400-38443400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr19:38441400-38456800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr19:38441600-38443600	Weak transcription	NH-A	brain
46	chr19:38441600-38443800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr19:38441600-38445200	Enhancers	Osteobl	bone
48	chr19:38441600-38449600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr19:38441800-38443400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:38441800-38443400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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