Variant report

Variant	rs1862371
Chromosome Location	chr19:39122923-39122924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39106830..39111691-chr19:39117375..39123240,7	MCF-7	breast:
2	chr19:39114934..39116951-chr19:39122867..39124583,2	K562	blood:
3	chr19:39109264..39111637-chr19:39122200..39124366,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178982	Chromatin interaction
ENSG00000104814	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10445564	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12976749	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs12977469	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13345885	1.00[CEU][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs1978443	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs2232992	0.87[CEU][hapmap];0.96[TSI][hapmap]
rs2287732	1.00[CEU][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs2287733	1.00[CEU][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs3786834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4592774	0.81[EUR][1000 genomes]
rs62120358	0.89[EUR][1000 genomes]
rs7251456	0.81[CEU][hapmap]
rs750438	0.94[ASW][hapmap];0.94[CEU][hapmap];0.93[GIH][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs888994	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9304576	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	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
6	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
7	nsv911667	chr19:39119898-39143289	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1862371	SELV	cis	parietal	SCAN
rs1862371	PLAUR	cis	cerebellum	SCAN
rs1862371	ZFP36	cis	parietal	SCAN
rs1862371	LYPD4	cis	parietal	SCAN
rs1862371	GSK3A	cis	cerebellum	SCAN
rs1862371	TMEM145	cis	parietal	SCAN
rs1862371	AP2S1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39111000-39124000	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr19:39111000-39124400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
3	chr19:39111000-39124600	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr19:39111000-39125000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:39111000-39127000	Strong transcription	Thymus	Thymus
6	chr19:39111000-39127400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr19:39111000-39128800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr19:39111200-39123600	Strong transcription	Osteobl	bone
9	chr19:39111200-39123800	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr19:39111200-39123800	Strong transcription	Primary B cells from peripheral blood	blood
11	chr19:39111200-39123800	Strong transcription	Primary T cells from cord blood	blood
12	chr19:39111200-39124000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:39111200-39124000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:39111200-39124000	Strong transcription	Liver	Liver
15	chr19:39111200-39124000	Strong transcription	Brain Angular Gyrus	brain
16	chr19:39111200-39124000	Strong transcription	Placenta	Placenta
17	chr19:39111200-39124000	Strong transcription	Fetal Thymus	thymus
18	chr19:39111200-39124000	Strong transcription	Left Ventricle	heart
19	chr19:39111200-39124000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr19:39111200-39124200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:39111200-39124200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr19:39111200-39124200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:39111200-39124200	Strong transcription	Brain Germinal Matrix	brain
24	chr19:39111200-39124200	Strong transcription	Fetal Brain Female	brain
25	chr19:39111200-39124200	Strong transcription	Lung	lung
26	chr19:39111200-39124400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:39111200-39124400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:39111200-39124400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr19:39111200-39124400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:39111200-39124400	Strong transcription	Adipose Nuclei	Adipose
31	chr19:39111200-39124400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr19:39111200-39124600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:39111200-39125000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr19:39111200-39125000	Strong transcription	Duodenum Mucosa	Duodenum
35	chr19:39111200-39125000	Strong transcription	Fetal Muscle Leg	muscle
36	chr19:39111200-39125200	Weak transcription	Fetal Heart	heart
37	chr19:39111200-39125400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr19:39111200-39126600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr19:39111200-39127600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr19:39111200-39127600	Strong transcription	Brain Anterior Caudate	brain
41	chr19:39111200-39130400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr19:39111200-39130800	Strong transcription	Fetal Stomach	stomach
43	chr19:39111200-39131000	Weak transcription	Right Atrium	heart
44	chr19:39111400-39123800	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr19:39111400-39123800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:39111400-39124000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr19:39111400-39124800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr19:39111400-39124800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr19:39111600-39124000	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr19:39111600-39124000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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