Variant report

Variant	rs234327
Chromosome Location	chr19:40503957-40503958
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40475223..40478471-chr19:40501440..40504433,4	MCF-7	breast:
2	chr19:40474074..40479560-chr19:40500872..40505885,15	K562	blood:
3	chr19:40471803..40479510-chr19:40500414..40506141,13	K562	blood:

Variant related genes	Relation type
ENSG00000013275	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10403646	0.81[AMR][1000 genomes]
rs10410695	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418448	1.00[EUR][1000 genomes]
rs10419218	1.00[EUR][1000 genomes]
rs10420514	1.00[EUR][1000 genomes]
rs10420687	1.00[EUR][1000 genomes]
rs10421243	1.00[EUR][1000 genomes]
rs10423298	1.00[EUR][1000 genomes]
rs10423800	1.00[EUR][1000 genomes]
rs10427117	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11883159	1.00[EUR][1000 genomes]
rs13382054	1.00[EUR][1000 genomes]
rs170898	0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234297	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234307	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs234312	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234316	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234319	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234321	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234322	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234339	0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234342	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234359	0.96[YRI][hapmap]
rs2531363	0.85[YRI][hapmap]
rs2542302	0.89[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2542311	0.89[YRI][hapmap];0.84[AMR][1000 genomes]
rs28661993	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28776318	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28832070	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs337795	1.00[EUR][1000 genomes]
rs337796	0.81[YRI][hapmap]
rs57342065	1.00[EUR][1000 genomes]
rs58348431	1.00[EUR][1000 genomes]
rs59707868	1.00[EUR][1000 genomes]
rs60631264	1.00[EUR][1000 genomes]
rs61424085	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245930	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7250945	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7257627	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258111	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258718	0.81[AMR][1000 genomes]
rs73930675	1.00[EUR][1000 genomes]
rs73930678	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73930679	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8111518	1.00[EUR][1000 genomes]
rs8111741	1.00[EUR][1000 genomes]
rs9630860	1.00[EUR][1000 genomes]
rs9630868	1.00[EUR][1000 genomes]
rs9783944	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	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

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40501800-40504000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:40502200-40504000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr19:40503000-40504000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr19:40503000-40504800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr19:40503200-40504000	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr19:40503200-40504000	Flanking Active TSS	Fetal Brain Female	brain
7	chr19:40503200-40504000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr19:40503200-40504000	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr19:40503200-40504000	Flanking Active TSS	Dnd41	blood
10	chr19:40503400-40504000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:40503400-40504000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:40503400-40504000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr19:40503400-40504000	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr19:40503400-40504000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
15	chr19:40503400-40504000	Flanking Active TSS	Brain Substantia Nigra	brain
16	chr19:40503400-40504000	Flanking Active TSS	Colon Smooth Muscle	Colon
17	chr19:40503400-40504000	Flanking Active TSS	Fetal Lung	lung
18	chr19:40503400-40504000	Enhancers	Placenta Amnion	Placenta Amnion
19	chr19:40503400-40504000	Flanking Active TSS	Thymus	Thymus
20	chr19:40503400-40504000	Flanking Active TSS	GM12878-XiMat	blood
21	chr19:40503400-40504000	Flanking Active TSS	K562	blood
22	chr19:40503600-40504000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr19:40503600-40504000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:40503600-40504000	Enhancers	Primary B cells from cord blood	blood
25	chr19:40503600-40504000	Enhancers	Primary B cells from peripheral blood	blood
26	chr19:40503600-40504000	Enhancers	Primary T cells fromperipheralblood	blood
27	chr19:40503600-40504000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr19:40503600-40504000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:40503600-40504000	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr19:40503600-40504000	Flanking Active TSS	HepG2	liver
31	chr19:40503600-40504200	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr19:40503600-40504400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:40503600-40504600	Enhancers	HMEC	breast
34	chr19:40503600-40504600	Enhancers	NHDF-Ad	bronchial
35	chr19:40503600-40504600	Enhancers	NHEK	skin
36	chr19:40503600-40505000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:40503600-40507000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:40503600-40507400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:40503600-40511800	Weak transcription	Ovary	ovary
40	chr19:40503600-40511800	Weak transcription	Spleen	Spleen
41	chr19:40503600-40512000	Weak transcription	Esophagus	oesophagus
42	chr19:40503600-40512400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:40503600-40513000	Weak transcription	Placenta	Placenta
44	chr19:40503600-40514000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:40503600-40519200	Weak transcription	Small Intestine	intestine
46	chr19:40503800-40504000	Enhancers	Primary hematopoietic stem cells	blood
47	chr19:40503800-40504000	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr19:40503800-40504000	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr19:40503800-40504000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:40503800-40504000	Enhancers	Cortex derived primary cultured neurospheres	brain

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