Variant report

Variant	rs4802888
Chromosome Location	chr19:39297560-39297561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10417292	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250734	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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	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
4	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
5	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
6	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
7	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4802888	LGALS7	cis	Skin Sun Exposed Lower leg	GTEx
rs4802888	LGALS7	cis	Esophagus Mucosa	GTEx

Chromatin state (count:70 , 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	chr19:39283600-39305600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:39283600-39305800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:39283600-39305800	Weak transcription	Brain Hippocampus Middle	brain
6	chr19:39283600-39305800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr19:39283800-39306000	Weak transcription	Primary B cells from cord blood	blood
8	chr19:39284000-39305600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:39284000-39318200	Weak transcription	Fetal Kidney	kidney
10	chr19:39284200-39305800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr19:39285200-39309400	Weak transcription	Fetal Heart	heart
12	chr19:39290200-39305800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:39290600-39297600	Weak transcription	A549	lung
14	chr19:39290800-39310600	Weak transcription	HMEC	breast
15	chr19:39291200-39307400	Weak transcription	Fetal Lung	lung
16	chr19:39291400-39305600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr19:39292000-39305800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr19:39292400-39300400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr19:39292600-39301800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr19:39292600-39303800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr19:39292600-39305800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:39292800-39303800	Weak transcription	Fetal Muscle Leg	muscle
23	chr19:39292800-39305800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:39292800-39306000	Weak transcription	Brain Anterior Caudate	brain
25	chr19:39293000-39305200	Weak transcription	Primary T cells from cord blood	blood
26	chr19:39294400-39299400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:39294400-39301800	Weak transcription	Small Intestine	intestine
28	chr19:39294600-39309800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:39294800-39299400	Weak transcription	Gastric	stomach
30	chr19:39294800-39302600	Weak transcription	Liver	Liver
31	chr19:39294800-39309800	Weak transcription	Psoas Muscle	Psoas
32	chr19:39295000-39300400	Weak transcription	Pancreas	Pancrea
33	chr19:39295000-39303000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:39295000-39303000	Weak transcription	Placenta	Placenta
35	chr19:39295000-39305600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:39295000-39305800	Weak transcription	Adipose Nuclei	Adipose
37	chr19:39295200-39302800	Weak transcription	Fetal Stomach	stomach
38	chr19:39296000-39300400	Genic enhancers	Fetal Intestine Small	intestine
39	chr19:39296000-39305800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr19:39296200-39305000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr19:39296200-39307000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr19:39296200-39318200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr19:39296400-39297600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:39296400-39297600	Weak transcription	HepG2	liver
45	chr19:39296400-39297800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr19:39296400-39297800	Strong transcription	Fetal Intestine Large	intestine
47	chr19:39296400-39298000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr19:39296400-39298200	Genic enhancers	Duodenum Mucosa	Duodenum
49	chr19:39296400-39298800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr19:39296400-39299000	Weak transcription	Lung	lung

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