Variant report

Variant	rs399405
Chromosome Location	chr19:40580426-40580427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40577512..40581181-chr19:40595512..40598520,4	K562	blood:
2	chr19:40473843..40476809-chr19:40580140..40582711,2	K562	blood:
3	chr19:40561659..40563335-chr19:40578220..40580556,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269296	Chromatin interaction
ENSG00000197782	Chromatin interaction
ENSG00000128000	Chromatin interaction
ENSG00000269749	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10414087	1.00[ASN][1000 genomes]
rs10418532	1.00[ASN][1000 genomes]
rs10421829	1.00[CHB][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10424773	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11881677	1.00[ASN][1000 genomes]
rs11882464	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11882490	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs163212	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973959	1.00[CHB][hapmap]
rs17756648	0.83[ASN][1000 genomes]
rs234329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234347	1.00[CHB][hapmap]
rs234348	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs234362	1.00[CHB][hapmap]
rs234363	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs234367	1.00[CHB][hapmap]
rs234369	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs2531363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28669038	1.00[ASN][1000 genomes]
rs337796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383975	1.00[ASN][1000 genomes]
rs420413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445379	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517342	1.00[ASN][1000 genomes]
rs520877	1.00[ASN][1000 genomes]
rs526467	1.00[ASN][1000 genomes]
rs532235	1.00[ASN][1000 genomes]
rs563703	1.00[ASN][1000 genomes]
rs589279	1.00[ASN][1000 genomes]
rs589404	1.00[ASN][1000 genomes]
rs60798356	0.87[EUR][1000 genomes]
rs62106576	1.00[ASN][1000 genomes]
rs62106577	1.00[ASN][1000 genomes]
rs62106578	1.00[ASN][1000 genomes]
rs62106580	0.83[ASN][1000 genomes]
rs62106581	0.83[ASN][1000 genomes]
rs62106584	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62106585	1.00[ASN][1000 genomes]
rs62106586	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62106587	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62106588	1.00[ASN][1000 genomes]
rs62106589	1.00[ASN][1000 genomes]
rs62106590	1.00[ASN][1000 genomes]
rs62106591	1.00[ASN][1000 genomes]
rs62106625	1.00[ASN][1000 genomes]
rs62106626	1.00[ASN][1000 genomes]
rs62108934	1.00[ASN][1000 genomes]
rs62110063	1.00[ASN][1000 genomes]
rs623196	1.00[ASN][1000 genomes]
rs636313	1.00[ASN][1000 genomes]
rs649239	1.00[ASN][1000 genomes]
rs6508931	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6508932	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs667850	1.00[ASN][1000 genomes]
rs7250244	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7250298	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7259136	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7260610	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73551672	0.83[ASN][1000 genomes]
rs73553618	1.00[ASN][1000 genomes]
rs8103746	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8103807	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8105260	1.00[ASN][1000 genomes]
rs8108062	1.00[ASN][1000 genomes]
rs8108857	1.00[ASN][1000 genomes]

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	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer 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	43 gene(s)	inside rSNPs	diseases
2	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40574400-40582400	Weak transcription	Fetal Stomach	stomach
2	chr19:40578600-40586200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
3	chr19:40578600-40586600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr19:40578600-40586600	ZNF genes & repeats	Liver	Liver
5	chr19:40578600-40586600	ZNF genes & repeats	A549	lung
6	chr19:40578600-40586800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:40578600-40590400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:40578800-40581000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:40578800-40582000	Strong transcription	Dnd41	blood
10	chr19:40578800-40582400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr19:40578800-40582600	Strong transcription	Colonic Mucosa	Colon
12	chr19:40578800-40583600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
13	chr19:40578800-40586600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
14	chr19:40578800-40587200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:40579000-40583200	ZNF genes & repeats	NH-A	brain
16	chr19:40579000-40583400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
17	chr19:40579000-40583600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
18	chr19:40579000-40583600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
19	chr19:40579000-40584600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
20	chr19:40579000-40586600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
21	chr19:40579000-40587000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:40579000-40587000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
23	chr19:40579200-40580800	Weak transcription	Stomach Mucosa	stomach
24	chr19:40579200-40581400	ZNF genes & repeats	HSMMtube	muscle
25	chr19:40579200-40581600	Strong transcription	Fetal Brain Female	brain
26	chr19:40579200-40581800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr19:40579200-40583400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
28	chr19:40579200-40583600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:40579200-40583600	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr19:40579200-40583800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
31	chr19:40579200-40583800	ZNF genes & repeats	Fetal Lung	lung
32	chr19:40579200-40583800	ZNF genes & repeats	HSMM	muscle
33	chr19:40579200-40584600	ZNF genes & repeats	Fetal Muscle Leg	muscle
34	chr19:40579200-40585000	ZNF genes & repeats	Primary B cells from cord blood	blood
35	chr19:40579200-40585600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
36	chr19:40579200-40585600	ZNF genes & repeats	Adipose Nuclei	Adipose
37	chr19:40579200-40585800	ZNF genes & repeats	Primary T cells from cord blood	blood
38	chr19:40579200-40586600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
39	chr19:40579200-40586600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
40	chr19:40579200-40586800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:40579200-40586800	ZNF genes & repeats	GM12878-XiMat	blood
42	chr19:40579200-40589600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:40579400-40582200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
44	chr19:40579400-40583200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
45	chr19:40579400-40583200	ZNF genes & repeats	HMEC	breast
46	chr19:40579400-40583400	ZNF genes & repeats	Osteobl	bone
47	chr19:40579400-40583600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:40579400-40585000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
49	chr19:40579400-40585400	Strong transcription	HepG2	liver
50	chr19:40579400-40590400	Strong transcription	Cortex derived primary cultured neurospheres	brain

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