Variant report

Variant	rs4802112
Chromosome Location	chr19:41734490-41734491
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41730763..41733652-chr19:41734170..41736394,3	K562	blood:
2	chr19:41732801..41734640-chr19:41767738..41769811,2	K562	blood:
3	chr19:41733057..41734716-chr19:41742855..41744985,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167601	Chromatin interaction
ENSG00000105323	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10421990	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs11879562	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs11882467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12327659	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs12462203	0.95[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs12975585	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12978098	0.84[ASN][1000 genomes]
rs12978323	0.94[CEU][hapmap];0.90[CHB][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs12979764	0.84[ASN][1000 genomes]
rs12980248	0.84[ASN][1000 genomes]
rs12980267	0.89[CEU][hapmap]
rs12980480	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs12983047	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs12984621	0.82[ASN][1000 genomes]
rs1865051	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1865053	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs1946612	0.89[CEU][hapmap]
rs2304230	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs2304234	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs3745295	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs3752705	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs3760659	0.89[CEU][hapmap]
rs3786555	0.85[ASN][1000 genomes]
rs3816052	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs3826714	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4456618	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs4802111	0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4802113	0.95[CHB][hapmap]
rs4802115	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4803448	0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4803449	0.80[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4803451	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6508974	0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6957	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs7245398	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs7246525	0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs7248164	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs7250883	0.89[CEU][hapmap]
rs7257310	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs7258749	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs8105161	0.88[JPT][hapmap]
rs8109167	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs8109627	0.90[CHB][hapmap];0.88[JPT][hapmap]

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	nsv911768	chr19:41680424-41748753	Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3452160	chr19:41734412-41737910	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3353863	chr19:41734412-41738010	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4802112	SLC1A5	cis	parietal	SCAN
rs4802112	SLC1A5	cis	cerebellum	SCAN
rs4802112	SLC6A16	cis	cerebellum	SCAN
rs4802112	FLT3LG	cis	cerebellum	SCAN
rs4802112	FOSB	cis	parietal	SCAN
rs4802112	BAX	cis	cerebellum	SCAN
rs4802112	MAGIX	trans	cerebellum	SCAN
rs4802112	CCDC9	cis	cerebellum	SCAN
rs4802112	FOXA3	cis	cerebellum	SCAN
rs4802112	ERF	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41730200-41762600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41732600-41768800	Weak transcription	Small Intestine	intestine
3	chr19:41732800-41735800	Weak transcription	Fetal Lung	lung
4	chr19:41732800-41736200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:41732800-41739200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:41732800-41742800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:41732800-41745200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:41733000-41735400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:41733000-41735600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:41733000-41735600	Weak transcription	Fetal Kidney	kidney
11	chr19:41733000-41736000	Weak transcription	Lung	lung
12	chr19:41733000-41736000	Genic enhancers	NHDF-Ad	bronchial
13	chr19:41733000-41736200	Weak transcription	Pancreas	Pancrea
14	chr19:41733000-41736400	Weak transcription	Brain Angular Gyrus	brain
15	chr19:41733000-41736400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr19:41733000-41736600	Weak transcription	Aorta	Aorta
17	chr19:41733000-41736600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr19:41733000-41736600	Weak transcription	Fetal Stomach	stomach
19	chr19:41733000-41738600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr19:41733000-41739200	Weak transcription	Placenta	Placenta
21	chr19:41733000-41739400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr19:41733000-41739400	Weak transcription	Ovary	ovary
23	chr19:41733000-41740200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr19:41733000-41743000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:41733000-41743200	Weak transcription	Right Ventricle	heart
26	chr19:41733000-41743600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr19:41733000-41743600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr19:41733000-41743600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:41733000-41743600	Weak transcription	Esophagus	oesophagus
30	chr19:41733000-41743600	Weak transcription	Spleen	Spleen
31	chr19:41733000-41743800	Weak transcription	Colonic Mucosa	Colon
32	chr19:41733000-41744200	Weak transcription	Gastric	stomach
33	chr19:41733000-41745200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:41733200-41735000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr19:41733200-41735000	Strong transcription	NHEK	skin
36	chr19:41733200-41735600	Strong transcription	HSMM	muscle
37	chr19:41733200-41735600	Strong transcription	Osteobl	bone
38	chr19:41733200-41736200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:41733200-41736600	Genic enhancers	A549	lung
40	chr19:41733200-41738000	Weak transcription	Colon Smooth Muscle	Colon
41	chr19:41733200-41738800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr19:41733200-41739400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr19:41733200-41739400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr19:41733200-41739600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr19:41733200-41740600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr19:41733200-41741400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr19:41733200-41745400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr19:41733200-41746000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr19:41733200-41749400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:41733200-41767200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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