Variant report

Variant	rs8109718
Chromosome Location	chr19:40447840-40447841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40439263..40441192-chr19:40446766..40448427,2	K562	blood:
2	chr19:40445775..40448041-chr19:40449337..40452328,2	MCF-7	breast:
3	chr19:40446423..40448525-chr19:40595370..40597652,2	MCF-7	breast:
4	chr12:53840252..53841772-chr19:40447090..40448611,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269296	Chromatin interaction
ENSG00000197782	Chromatin interaction
ENSG00000269749	Chromatin interaction
ENSG00000187534	Chromatin interaction
ENSG00000090920	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs170900	0.89[GIH][hapmap]
rs186816	0.83[GIH][hapmap]
rs2231738	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs234365	0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs234370	0.88[GIH][hapmap]
rs2355720	0.83[ASW][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.98[MKK][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs337799	0.81[GIH][hapmap]
rs371500	0.88[GIH][hapmap]
rs3754	0.82[ASN][1000 genomes]
rs3760919	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3760923	0.83[ASW][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.98[MKK][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3786938	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3826919	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs421533	0.88[GIH][hapmap]
rs424365	0.86[ASN][1000 genomes]
rs426950	0.88[GIH][hapmap]
rs427461	0.83[CHB][hapmap]
rs459091	0.88[GIH][hapmap]
rs59030876	0.81[AFR][1000 genomes]
rs7249286	0.89[GIH][hapmap]
rs7249890	0.84[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8105066	0.88[GIH][hapmap]
rs8106269	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109879	0.94[ASN][1000 genomes]
rs9749001	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv510766	chr19:40344356-40453018	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	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
6	nsv978815	chr19:40443651-40449610	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40441200-40449000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:40442000-40450400	Weak transcription	Brain Substantia Nigra	brain
3	chr19:40442400-40449000	Weak transcription	Pancreas	Pancrea
4	chr19:40442400-40450400	Weak transcription	Lung	lung
5	chr19:40446600-40449200	Flanking Active TSS	Dnd41	blood
6	chr19:40446800-40448400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:40446800-40448400	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr19:40446800-40448400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr19:40446800-40448400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr19:40446800-40448800	Enhancers	Primary hematopoietic stem cells	blood
11	chr19:40446800-40451600	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr19:40446800-40453000	Enhancers	Fetal Intestine Large	intestine
13	chr19:40446800-40453000	Enhancers	Stomach Mucosa	stomach
14	chr19:40447000-40448000	Enhancers	Gastric	stomach
15	chr19:40447000-40448200	Enhancers	Brain Germinal Matrix	brain
16	chr19:40447000-40448400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr19:40447000-40448400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:40447000-40448400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr19:40447000-40448400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr19:40447000-40448600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:40447000-40448600	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr19:40447000-40448600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr19:40447000-40448600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr19:40447000-40449200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:40447000-40449200	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr19:40447000-40449800	Enhancers	Fetal Muscle Leg	muscle
27	chr19:40447000-40450400	Enhancers	Thymus	Thymus
28	chr19:40447000-40450800	Enhancers	Fetal Thymus	thymus
29	chr19:40447200-40448400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr19:40447200-40448400	Enhancers	Fetal Brain Female	brain
31	chr19:40447200-40449600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr19:40447200-40453000	Enhancers	Fetal Intestine Small	intestine
33	chr19:40447400-40448000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:40447400-40448200	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr19:40447400-40449000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:40447400-40449000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:40447400-40449000	Weak transcription	Esophagus	oesophagus
38	chr19:40447400-40449000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:40447400-40449600	Weak transcription	Placenta	Placenta
40	chr19:40447400-40450200	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr19:40447400-40451200	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr19:40447600-40448000	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr19:40447600-40448000	Enhancers	HMEC	breast
44	chr19:40447600-40448000	Flanking Active TSS	HUVEC	blood vessel
45	chr19:40447600-40448200	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr19:40447600-40448200	Weak transcription	Liver	Liver
47	chr19:40447600-40448400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:40447600-40448400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr19:40447600-40448400	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr19:40447600-40448400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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