Variant report

Variant	rs4802887
Chromosome Location	chr19:39296319-39296320
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39295644..39297355-chr19:39298122..39300967,2	MCF-7	breast:
2	chr19:39221109..39222867-chr19:39294750..39296802,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171747	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10426289	0.84[JPT][hapmap]
rs1078734	0.84[JPT][hapmap]
rs13344413	1.00[ASW][hapmap]
rs2279143	0.80[JPT][hapmap]
rs2303040	0.86[ASW][hapmap]
rs3786839	0.86[ASW][hapmap]
rs4802886	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508816	0.89[JPT][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	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4802887	HNRNPUL1	cis	cerebellum	SCAN
rs4802887	ZC3H4	cis	parietal	SCAN
rs4802887	LGALS7B	cis	Skin Sun Exposed Lower leg	GTEx
rs4802887	TMEM91	cis	cerebellum	SCAN
rs4802887	C19orf47	cis	cerebellum	SCAN
rs4802887	CEACAM7	cis	cerebellum	SCAN
rs4802887	LGALS7	cis	Esophagus Mucosa	GTEx
rs4802887	ERCC1	cis	cerebellum	SCAN
rs4802887	ZNF575	cis	parietal	SCAN

Chromatin state (count:72 , 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	chr19:39292600-39296400	Strong transcription	Colonic Mucosa	Colon
20	chr19:39292600-39301800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr19:39292600-39303800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr19:39292600-39305800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr19:39292800-39303800	Weak transcription	Fetal Muscle Leg	muscle
24	chr19:39292800-39305800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:39292800-39306000	Weak transcription	Brain Anterior Caudate	brain
26	chr19:39293000-39305200	Weak transcription	Primary T cells from cord blood	blood
27	chr19:39294400-39299400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr19:39294400-39301800	Weak transcription	Small Intestine	intestine
29	chr19:39294600-39309800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:39294800-39296400	Genic enhancers	Fetal Intestine Large	intestine
31	chr19:39294800-39299400	Weak transcription	Gastric	stomach
32	chr19:39294800-39302600	Weak transcription	Liver	Liver
33	chr19:39294800-39309800	Weak transcription	Psoas Muscle	Psoas
34	chr19:39295000-39300400	Weak transcription	Pancreas	Pancrea
35	chr19:39295000-39303000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr19:39295000-39303000	Weak transcription	Placenta	Placenta
37	chr19:39295000-39305600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr19:39295000-39305800	Weak transcription	Adipose Nuclei	Adipose
39	chr19:39295200-39302800	Weak transcription	Fetal Stomach	stomach
40	chr19:39295400-39296600	Enhancers	HUVEC	blood vessel
41	chr19:39295800-39296400	Enhancers	Primary B cells from peripheral blood	blood
42	chr19:39295800-39296400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr19:39296000-39296400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:39296000-39296400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr19:39296000-39296400	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr19:39296000-39296400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr19:39296000-39296400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:39296000-39296400	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
49	chr19:39296000-39296400	Enhancers	Esophagus	oesophagus
50	chr19:39296000-39296400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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