Variant report

Variant	rs2278009
Chromosome Location	chr19:39327856-39327857
allele	A/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	chr19:39326299..39328911-chr19:39388226..39390640,3	K562	blood:
2	chr19:39326299..39328674-chr19:39389140..39390810,2	K562	blood:
3	chr19:39326367..39329872-chr19:39419342..39422625,3	MCF-7	breast:
4	chr19:39137584..39140325-chr19:39327324..39331607,4	MCF-7	breast:
5	chr19:39218553..39228703-chr19:39324875..39331730,17	MCF-7	breast:
6	chr19:39223964..39228282-chr19:39327392..39332302,8	MCF-7	breast:
7	chr19:39325391..39328182-chr19:39375242..39377449,2	K562	blood:
8	chr19:39183521..39187102-chr19:39327849..39329398,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction
ENSG00000104825	Chromatin interaction
ENSG00000267375	Chromatin interaction
ENSG00000068903	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000128626	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1001413	1.00[CHB][hapmap]
rs1103435	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11668766	0.80[CEU][hapmap]
rs2113123	0.95[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes]
rs2113124	0.96[EUR][1000 genomes]
rs2278011	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318459	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28496951	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs35812434	0.81[EUR][1000 genomes]
rs6508822	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67859595	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7246134	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255774	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8100220	0.96[CHB][hapmap];0.86[JPT][hapmap]
rs8104416	0.95[EUR][1000 genomes]
rs8104420	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[EUR][1000 genomes]
rs862455	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs862459	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs862464	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9789283	0.89[EUR][1000 genomes]

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	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv961291	chr19:39324891-39329561	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2278009	HNRNPL	N/A	lymphoblastoid	RTeQTL
rs2278009	HNRNPL	Cis_1M	lymphoblastoid	RTeQTL
rs2278009	ECH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39322400-39331800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39323000-39334600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:39324600-39338000	Strong transcription	Fetal Brain Female	brain
4	chr19:39325000-39334000	Strong transcription	Fetal Stomach	stomach
5	chr19:39325200-39331600	Strong transcription	Primary T cells from cord blood	blood
6	chr19:39325400-39328600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:39325400-39329200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr19:39325400-39329800	Genic enhancers	Fetal Lung	lung
9	chr19:39325400-39331200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:39325400-39331600	Strong transcription	Fetal Thymus	thymus
11	chr19:39325400-39332000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:39325400-39332200	Strong transcription	Thymus	Thymus
13	chr19:39325400-39336800	Strong transcription	Brain Substantia Nigra	brain
14	chr19:39325400-39337800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:39325400-39337800	Strong transcription	Brain Cingulate Gyrus	brain
16	chr19:39325400-39338000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr19:39325400-39338200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr19:39325400-39338200	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:39325600-39329400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr19:39325600-39333600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:39325600-39338000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:39325800-39328400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr19:39325800-39330800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:39326000-39328000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr19:39326000-39328200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:39326000-39328200	Genic enhancers	Stomach Smooth Muscle	stomach
27	chr19:39326000-39328400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:39326000-39328600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:39326000-39328600	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr19:39326000-39329200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:39326000-39331000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr19:39326000-39331200	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr19:39326000-39332200	Genic enhancers	Placenta	Placenta
34	chr19:39326000-39332600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr19:39326000-39332600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr19:39326000-39333800	Strong transcription	Colonic Mucosa	Colon
37	chr19:39326000-39334000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:39326000-39336200	Strong transcription	Brain Hippocampus Middle	brain
39	chr19:39326000-39336600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr19:39326000-39337000	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr19:39326000-39337800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:39326000-39338000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:39326000-39338000	Strong transcription	Brain Anterior Caudate	brain
44	chr19:39326000-39338000	Strong transcription	HSMM	muscle
45	chr19:39326000-39338200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr19:39326000-39338200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr19:39326000-39338200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr19:39326000-39338200	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr19:39326000-39338200	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr19:39326000-39338400	Strong transcription	iPS-15b Cell Line	embryonic stem cell

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