Variant report

Variant	rs9990934
Chromosome Location	chr4:15473771-15473772
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10000250	0.80[CEU][hapmap]
rs10012583	0.88[ASN][1000 genomes]
rs10022530	0.87[CEU][hapmap]
rs13108125	0.91[ASN][1000 genomes]
rs13131227	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2286976	0.86[CHD][hapmap]
rs4140933	0.81[YRI][hapmap]
rs4140934	0.84[YRI][hapmap]
rs4423869	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs4698109	0.90[ASN][1000 genomes]
rs4698112	0.81[YRI][hapmap]
rs6810461	0.88[YRI][hapmap]
rs719993	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7682982	0.86[CHD][hapmap]
rs9992835	0.94[ASN][1000 genomes]
rs9993580	0.87[CEU][hapmap]
rs9994702	0.87[CEU][hapmap]
rs9998686	0.81[YRI][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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9990934	FAM200B	cis	parietal	SCAN
rs9990934	CD38	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15471800-15474400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:15471800-15480800	Weak transcription	Pancreas	Pancrea
3	chr4:15471800-15481000	Weak transcription	Spleen	Spleen
4	chr4:15472000-15474400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:15472200-15473800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:15472200-15473800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:15472200-15473800	Weak transcription	HSMMtube	muscle
8	chr4:15472200-15474000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:15472200-15475600	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr4:15472200-15475600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr4:15472200-15477800	Weak transcription	Left Ventricle	heart
12	chr4:15472200-15480600	Weak transcription	HSMM	muscle
13	chr4:15472200-15480800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:15472200-15480800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:15472200-15480800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:15472200-15480800	Weak transcription	Fetal Intestine Large	intestine
17	chr4:15472200-15480800	Weak transcription	Fetal Intestine Small	intestine
18	chr4:15472200-15480800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:15472200-15480800	Weak transcription	Lung	lung
20	chr4:15472600-15473800	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr4:15472600-15474400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:15472600-15477800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:15472600-15480800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr4:15472800-15475000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:15472800-15480800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:15472800-15480800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr4:15472800-15480800	Weak transcription	NHLF	lung
28	chr4:15473000-15474000	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr4:15473000-15474400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:15473000-15475200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr4:15473000-15477200	Weak transcription	Ovary	ovary
32	chr4:15473000-15477800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:15473000-15480400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:15473000-15480800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:15473000-15480800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr4:15473000-15480800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:15473000-15480800	Weak transcription	Fetal Kidney	kidney
38	chr4:15473000-15480800	Weak transcription	Psoas Muscle	Psoas
39	chr4:15473200-15473800	Active TSS	Stomach Smooth Muscle	stomach
40	chr4:15473200-15474000	Enhancers	Rectal Smooth Muscle	rectum
41	chr4:15473200-15474400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr4:15473200-15477200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr4:15473200-15477400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:15473200-15477600	Weak transcription	Fetal Muscle Leg	muscle
45	chr4:15473200-15477800	Weak transcription	Adipose Nuclei	Adipose
46	chr4:15473200-15477800	Weak transcription	Aorta	Aorta
47	chr4:15473200-15480800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:15473200-15480800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr4:15473200-15480800	Weak transcription	Fetal Heart	heart
50	chr4:15473200-15480800	Weak transcription	Fetal Lung	lung

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