Variant report

Variant	rs10403583
Chromosome Location	chr19:39291771-39291772
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39289399..39293459-chr19:39320493..39322736,5	MCF-7	breast:
2	chr19:39163941..39166485-chr19:39290106..39293059,2	K562	blood:

Variant related genes	Relation type
ENSG00000104823	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10422360	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10775532	0.81[MKK][hapmap]
rs11667149	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11670444	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11671359	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35116302	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802817	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4802853	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7255094	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8108748	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8111466	0.80[ASN][1000 genomes]
rs974454	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	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
4	nsv1061904	chr19:39249692-39302843	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	nsv911670	chr19:39250308-39322087	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv911671	chr19:39252238-39306425	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
7	nsv911672	chr19:39252238-39318006	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1058132	chr19:39279522-39302843	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10403583	LYPD3	cis	cerebellum	SCAN
rs10403583	PVR	cis	cerebellum	SCAN
rs10403583	LGALS7	cis	Esophagus Mucosa	GTEx
rs10403583	CEACAM6	cis	cerebellum	SCAN
rs10403583	LRIG1	trans	cerebellum	SCAN
rs10403583	CYP2F1	cis	cerebellum	SCAN
rs10403583	RNU6-140P	cis	Esophagus Mucosa	GTEx
rs10403583	LGALS7	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39283200-39305600	Weak transcription	Brain Angular Gyrus	brain
2	chr19:39283200-39305600	Weak transcription	Brain Substantia Nigra	brain
3	chr19:39283400-39294000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:39283400-39294000	Weak transcription	Pancreas	Pancrea
5	chr19:39283600-39291800	Weak transcription	Gastric	stomach
6	chr19:39283600-39292200	Weak transcription	Right Ventricle	heart
7	chr19:39283600-39292600	Weak transcription	Colonic Mucosa	Colon
8	chr19:39283600-39294000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:39283600-39296000	Weak transcription	Left Ventricle	heart
10	chr19:39283600-39296000	Weak transcription	Lung	lung
11	chr19:39283600-39296000	Weak transcription	Right Atrium	heart
12	chr19:39283600-39305600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:39283600-39305800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr19:39283600-39305800	Weak transcription	Brain Hippocampus Middle	brain
15	chr19:39283600-39305800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr19:39283800-39295800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr19:39283800-39295800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr19:39283800-39296000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr19:39283800-39306000	Weak transcription	Primary B cells from cord blood	blood
20	chr19:39284000-39291800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr19:39284000-39295800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr19:39284000-39305600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:39284000-39318200	Weak transcription	Fetal Kidney	kidney
24	chr19:39284200-39291800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:39284200-39294000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:39284200-39305800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr19:39285200-39309400	Weak transcription	Fetal Heart	heart
28	chr19:39288800-39292400	Weak transcription	Fetal Stomach	stomach
29	chr19:39289600-39296000	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr19:39289600-39296000	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr19:39289800-39295800	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr19:39290000-39296000	Weak transcription	Esophagus	oesophagus
33	chr19:39290200-39296000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:39290200-39296000	Strong transcription	Fetal Intestine Small	intestine
35	chr19:39290200-39305800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr19:39290400-39292400	Weak transcription	Small Intestine	intestine
37	chr19:39290600-39297600	Weak transcription	A549	lung
38	chr19:39290800-39295800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr19:39290800-39296000	Weak transcription	NHEK	skin
40	chr19:39290800-39310600	Weak transcription	HMEC	breast
41	chr19:39291000-39296000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:39291200-39294800	Strong transcription	Fetal Intestine Large	intestine
43	chr19:39291200-39296000	Weak transcription	Ovary	ovary
44	chr19:39291200-39307400	Weak transcription	Fetal Lung	lung
45	chr19:39291400-39292000	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr19:39291400-39292400	Strong transcription	Rectal Smooth Muscle	rectum
47	chr19:39291400-39294800	Strong transcription	Liver	Liver
48	chr19:39291400-39295000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr19:39291400-39296000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr19:39291400-39305600	Weak transcription	Primary T cells fromperipheralblood	blood

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